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1. 3 Mikrohartemessunc KorngroBenanalyse Feldname Feldwert C KomagraBenanalyse Beispiel TEM Aufnahme C3 Kalibrierbilder Modul Aufnahme C3 Gusseisen Datensatzname TEM Aufnahme thle eR EE aE Co i i ee C3 Fluorescence Imac Datensatz Nr 28 J Fluorescence Imac Ga Fikeranwendung patum 0311 2002 Ca Fiteranwendung o i Ca F vtendad Fnnall a H s H Beispieldatenbank 5 TEM Aufnahme 4 Beispieldatenbank TEM Aufnahme Archiving Images Choose View Step by step Step by step Work in the database window 1 Open either the example database which you can install together with your image analysis program or one of your own databases 2 If you need space for images or reports click in the database window button bar on the Narrow view button to reduce the database window gt Your image analysis program removes the form view and reduces the gallery to a narrow stripe gt Your image analysis program changes the size of the database window so that it takes up half of the document area The database window is posi tioned on the right of the image manager H TE 3 If you are mainly working inside the database click the Full view button in the database document s button bar gt Your image analysis program divides the database window into four sections E 4 In the tree structure mark the uppermost entry with
2. Choose View Set Default User Field Values Insert ote Record igand Document Load with Documents a ta a Perspective Archiving Images Archive data Background Information 49 Calibratic Arrange Fields E Fluoresc Copy Table Settings ExampleD atabase wiew Button Era Define Contest Menu Archive data Background Information Archiving e Temporary storage directory Storage Archiving allows you to archive older files from the current database on a CD or other data carriers The original data are subsequently deleted from the database You can of course continue to work with the entire database i e formulate queries or insert and load data The thumbnails of the stored records are still available If you load a stored record you will simply be asked to insert the appropriate storage medium Ony complete database folders are stored You can lock the database folder when storing Insertion of data into a locked database folder is then no longer possible Always use the wizard to secure data when archiving Never transfer data from a database in Windows Explorer This directory is used for temporary storage of the files when archiving the database Set up the directory for the database files and the temporary storage directory in the same partition on the main drive In this case the system checks the available space when inserting the data into the database As soon as
3. automatic scale bar zoom factor Alter scale bar properties 1 Select the Image gt Scale Bar gt Properties command 2 Select the Display tab in the Scale Bar Properties dialog box This is where you define what automatic scale bars you wish to have shown and where e Select the type of scale bar desired in the Scale bar selection group Be sides the usual horizontal scale bar there s a vertical scale bar and a pal ette bar to choose from The palette bar shows how colors and gray values correspond in false color images When using gray value images whose image intensity has been calibrated the values for the intensity are provid ed e Define where the automatic scale bar s are to be shown in the Show scale bar for group Have the scale bar shown in viewports onscreen Viewport printed out Printer or copy it into the clipboard Clipboard Any combina tion of the three application areas may be selected 3 Select the Format tab to define how the scale bar is to look e There are three types of different scale bars to choose from in the Scale bar styles group Scale bars may have a white or yellow or transparent frame Select any color to label the scale bar for transparent frames 4 Select the Size tab Show horizontal scale bars within images as well as vertical scale bars and palette bars too Palette bars show how colors and gray val ues correspond in false color images left In images with
4. the vertically orientated par Si ticles have been detected In the lower right image al only the black particles have Y iS 9 S been detected aama H ie AP G Y h lt i SS N ITP EE S X k a Navigat 1 Activate the magnifier before defining the particle filters so that even small UGE particles can be identified well in the image To do so click the bottom most i button in the viewport manager and select the first entry entitled Magnifier from the list of the available views Ha 2 Select the Analysis gt Define Measurements command 3 Should no particles have been detected yet In the Define Measurements dialog box click the Detect button 4 Select the parameter you wish to define a particle filter for in the Selected Measurements list e g Area a kx Image Analysis Measuring Particles Step by step gt The Filter Range group will become active The values in this group always refer to the currently active measurement parameter in the list of selected measurements 5 In the Filter Range group click the Get Minimum button next to the Min field to determine the minimum particle value gt The pointer will appear within the image 6 Leftclick on a typically small particle which should still be detected gt All particles whose area is smaller than the selected particle are shown in the overlay as hatched The hatched particles are no longer taken into consideration wh
5. Preparation Archiving Images Choose View Background Information Choose View Background Information Database window Several databases can be open simultaneously Each STAR database is repre sented in its own window You can choose between different window views when working with the database Standard full view Normally the database window is divided into four sections You can arrange the size of the individual sections as required to do so move the mouse pointer to the section edge and move it with the left mouse button depressed On the lower left you will find the tree structure in which the data is arranged The upper level is the name of the database Below this are the main entries which are characterized by the organizational ID of the database A maximum of three sub levels are allowed under a main entry Each type of document is identified by its own icon Doubleclicking on an entry extends or reduces the active level The record which is marked in the tree structure is displayed on the upper left Doubleclicking on the icon in the preview window jumps up to the next higher level in the tree structure On the lower right you will find a sheet with the columns Field name and Field value All the field information which you have selected with the Arrange Fields command for Form View is displayed here You will find the gallery view on the upper right of the database window It shows all records which are
6. Update Reinstall e Should you already have analySIS installed Setup offers you an update of the installation You should select this option to keep important program settings These settings include the calibration data for example Precalibrated input e When working with a light microscope the input channel can be precali channels brated This can however only be done with certain camera types such as the FireWire cameras from Olympus Soft Imaging Solutions for example Hardware e analySIS supports different types of microscopes stages and cameras installation Select your hardware during installation so that the correct drivers are in stalled gt After successful installation a program file with the links to the installed components is opened 8 You may now connect your FireWire camera to your computer oN 9 Doubleclick the program symbol to start the software e The icon to start analySIS can be dragged and dropped onto your desktop while you press the Ctrl key You can then conveniently open analySIS with one doubleclick A 10 Doubleclick on the Read Me icon for the latest information on analySIS Precalibrated inputs 37 Step by Step analySIS Installing analySIS Step by step Installing the network dongle These step by step instructions are only relevant when you use a network dongle In these instructions Server stands for the computer on which the network dongle and the license manager have been insta
7. 2 Activate the image window by simply leftclicking within the window e Ifthe header of the Images window is in color this means it is active 3 Select the Standard button bar gt Open command 4 Leftclick on the image file you wish to load 5 Drag the file directly onto any one of the image buffers while pressing the left mouse button drag amp drop gt The image buffer will show a preview of the image you have loaded 6 Repeat the last step as often as needed 7 To quit loading just click the Close button Li 18 First Steps Displaying multiple images Background information Use the mouse to drag amp drop images into the image buffer de sired MS Explorer a file man ager can also be used for drag amp drop loading Open Image 77 Look in Ee Images File name Aua Files of type T aac Displaying multiple images Background information Viewport The viewport manager enables you to influence the way images are dis played in the image win dow A viewport is a window in the image window where each of the loaded images or the live image is displayed You can divide the image window into numerous viewports thus displaying numerous images simultaneously Yiewport M anager x 1 2 Trl Image 2 a 4 Image 3 Image 4 Arrange View ports Opens the Display Properties dialog box Enables you for example to change the ap ties pearance of the viewp
8. 20 First Steps Displaying multiple images Step by step Press Ctrl Alt T to generate a test image It will have a color image overlay which displays current monitor resolu tion and other informa tion Press Ctrl Alt Shift T to generate a color test im age The test image is auto matically the same size as the active viewport The test image will al ways be displayed at 100 zoom The header shows the number of the image s image buffer 2 the image name Test and the current zoom factor 100 im a T21 X 2 Click the Arrange Viewports button to re define the number and arrangement of viewports Select a 1x2 arrangement gt The image window will be divided up into two viewports The test image is in the left viewport Image buffers will be reassigned Zoom factors will be set to Auto Though reduced in size somewhat the entire test image will be shown 3 Click the Single View button to display just one image in the image window the active viewport image gt The viewport arrangement and what image buffers are shown in which viewports remain unchanged 4 Select one of the entries of the Zoom Factor dropdown list or enter any zoom factor desired into the field directly e g 30 gt The test image will be reduced to 30 zoom The viewport will no longer be totally taken up by the image Where the patterned background starts in the viewport is where the image stops
9. Generally the images are inserted into a report in the way they are shown in the im age window For example this means that an 16 bit image is inserted into a report with the current display LUT LLZI 178 Report Generator Report objects Background information Print magnification Print magnification Print size Image size Rotate image The illustration shows the inserted image in three different available magnifications in the ob ject properties The im age object is the same size each time A frame indicates the size of the image object There are two different predefined magnifications showing different image seg ments If your image analysis program supports multidimensional image types you will find an additional tab in the image properties which enables you to determine which di mensions are to be acquired in the report for an empty image object An image s print size within a report depends on the image object properties selected and on image calibration The following is generally true print size print magnification x image size The print magnification is the absolute magnification at which the image is printed out on paper Your image analysis program determines print magnification via the print size and the absolute image size The print size is the size the image is printed on paper Without any automatic label ling the print size of the image will correspond exactly to the size of the
10. Pixel Any image you wish to calibrate after acquisition must of course contain a dis tance of known length e g a scale bar Use the Image gt Calibrate Image com mand To ensure that your images are correctly calibrated you must reset the magnification within your image analysis program before the first image acquisition and anytime you change the magnification on your microscope To redefine magnification for the active logical input simply use the Image gt Set Magnification command Your image analysis program can operate numerous light microscopes and electron microscopes via the remote control If you have a remote hook up your microscope s currently set magnification will be automatically read To activate the remote select the Remote gt On check box on the Image gt Configure Input gt Magnification tab Calibrate inputs This step by step instruction is only relevant if you have not selected an automatic XY calibration during the installation of your image analysis program You can also use this step by step instruction if you want to recalibrate objectives which were not provided during installation 1 Before starting the calibration check the acquisition conditions The following settings guarantee that you can execute a calibration without any problems e Select the Image gt Acquisition command to display the camera image live onscreen Acquiring images Calibrating inputs Step by step e Open t
11. Text objects in ob Object templates cannot include editable text objects If you wish to subsequently in ject templates sert a record object into a report you can only alter the texts within the text objects in the edit object mode Step by step Creating new field object templates The object template is to include two field objects of varying format One format is to indicate the magnification of each image The other differently formatted field ob jects are to contain information on the image database image 1 Load the image database which contains the images for your report 2 Select a record object and click the Edit Object Template button in the report z window button bar to switch over to the edit mode for object templates 3 Click the Field button in the Report Objects button bar to insert a standard field object into the record You will be creating a new object template for field objects based on this field object e You cannot insert field objects without an existing database This is be cause without a database no field information will be available You will re ceive an error message if a database is not open gt The Select Field dialog box will be opened This is where you ll find all da tabase fields that are defined in the active image database 4 Select any of the database fields and confirm via OK e When defining an object template you don t need to worry about selecting any particular database
12. Background information 8 Select the Live overlay check box to be able to write information into the image overlay during live acquisition The live overlay is also a necessary requirement for some of the other functions e g partial readout which you can activate in the camera controls 9 Select one of four display options in the Image scaling list 10 Confirm the settings you have made by clicking OK Acquiring images Background information Live acqui sition mode Acquiring snapshots Camera control 4 The functions available in the Camera Control dialog box will depend on what kind of camera you re using When us ing a ColorView Illu the dialog box appears as below In the live acquisition mode you see the live image in the active viewport The re quirements for the live acquisition are determined by the active input channel Use the live acquisition mode for focusing illuminating and positioning your specimen un der the microscope While in the live image mode only those commands that are rel evant in this mode are available to you Selecting the Image gt Snapshot command acquires a single image via the active log ical input channel and places it in the active image buffer Use this command to quit the live acquisition mode as well When an image is acquired additional image information is also saved e g calibra tion data and current input magnification Rightclick on an image buffer to access
13. Interactive Image Measurement Measuring Arbitrary Structures Step by step Examples of objects which can be located well with the magic wand Step by step This is how you define an object with the magic wand In by e ia y F Images 3 T 25 100 1 P Es ored cell nuclei are to be measured The mean aal R color value should also be acquired in addition to the area of the cell nuclei 1 Load the image you want to measure into the active image buffer 2 Select a zoom factor of 100 This is the best setting for the magic wand 3 When measuring a large image use the navigator to select the area of interest in the image before starting the measurement Click the bottom most button in the viewport manager and select the first entry entitled Navigator from the list of the available views By keeping the left mouse button depressed move the red frame in the viewport manager onto the object which is to be measured The navigator view in z We Voie manager always shows the entire image The red rectan gle shows which image section will be shown in the image window Se lect the image section of interest with the mouse directly from the thumb nail image shown Magnifier Viewport 4 Click the Measurements button located in the standard button bar to switch to the measurements environment m 5 Click the Magic Wand button located in the measurement button bar gt The pointer moves
14. gt The Database gt Administration gt Change Database Password command is available 3 Select the Database gt Administration gt Change Database Password command gt You will receive a warning that the database is lost if you forget the pass word gt The Change Database Password dialog box opens 4 Enter your password in the New Password field e You can enter up to 14 characters e The system is upper and lower case sensitive 5 Retype your password in the Retype password field gt The OK button is activated 6 Confirm the password by clicking OK e In future you can only open the database by using the correct password Change Database Password Old password Ok pooo New password tititi Cancel tl Help Retype password G6 96 Processing images Processing images Background Information Processing images Editing overlay Background Information Overlays Bitmap and vector graphic The figure shows a pixel line and a vector line greatly magnified The overlay is a vector graphic An image is made up of single pix els Overlay Layers Annotation layer Data layer Overlays contain labels highlighters e g an arrow or graphics e g your compa ny logo Many image analysis functions write measurement results in the overlay as well Overlays are placed over images like an overhead transparency The image in formation beneath the overlay rem
15. image analytical operations The mask has to be loaded into the mask image Maszk buffer Only those image areas which are covered by the white areas of the mask will have the operation applied to them Activating a mask e Image analysis to use a mask for image analytical operations the mask has to be activated This is done by rightclicking on the Mask operand in the operands box of the image manager Select the Enable Mask com mand in the context menu that appears e Detection a mask does not have to be active or enabled to use it for particle analysis All you need to do is select the Mask option in the Define Detection dialog box Step by step Setting a frame 1 Select the Image gt Set Frame command fa gt A red rectangle will denote the current frame in the image overlay gt The pointer is attached to the lower right hand corner of the frame 2 Press the left mouse button and pull the lower right hand corner of the frame until you reach the desired frame size 3 Move the frame to the desired position in the image 2 4 Click the right mouse button to set the frame m r gt As long as a frame is active the Enable Frame button will remain de ns pressed in the Standard button bar Press this button to turn the frame on or off gt The size and position of the current frame will be displayed in the sta tus bar Image Analysis Defining detection area Step by step Button Enable Frame Fie Ede rat
16. taining the original image following color coding Otherwise the Phase Analy sis command will be either not available because color coding a gray value im age results in a false color image or it produces a result you cannot use be cause color coding a true color image results in a new true color image for which the set thresholds are no longer applicable When defining thresholds for true color images in the dialog box for setting thresholds phases can be defined for either the RGB red green blue or HSI hue saturation intensity spaces Suitable phases are often easier to determine in the HSI space Executing a phase analysis 1 Acquire an image of a multi phase object which you wish to analyze Or simply load an existing image 3 A 2 Select the Image gt Set Thresholds command to define the gray value ranges for the separate phases 6E1 140 Image Analysis Phase analysis Step by step 3 Select the Auto Settings tab to have thresholds automatically calculated via the image histogram 4 Click the Set RO button to define a rectangular image area which will be evaluated for setting the thresholds e Make sure that all relevant image information is included in the image area you define The histogram in the dialog box will show the gray value distribution within the area defined only 5 Select the None option in the Background group to take all gray value rang es within the area defined into consi
17. 1000 Intensity 200 hue 200 Adjusting colors RGB 1 Select the Oper gt Adjust Colors gt Define RGB Adjustment command to adjust the red green and blue components of the active image 2 Select the Preview check box to be able to watch alterations as they occur with in the image Click the Window button to define an arbitrary rectangular area within the image for the preview e The preview window is only relevant while you define color adjustment When the defined color adjustment is conducted colors are adjusted for the entire image or if a frame has been set to the area within the frame e The first time you start up the default setting for the preview is for the whole image 3 Defining color adjustment parameters e Move one of the slide controls to the left to reduce that color within the im age e Move a slide controls to the right to increase that color within the image e A value of 0 means that a color component s original value remains unal tered 4 Click the Reset button to return to the original image as it was before you made any adjustments All parameters are reset to 0 5 Click the File button to save a set of parameters A parameter set you have saved can be reloaded anytime and used for color adjustment on any image 6 Click the Execute button to execute color adjustment using the current param eters gt The dialog box will be closed and the current preview image will be written into t
18. Fixed Scaling automatic set ting manual setting Black balance Sharpness Moni tor On Off Partial Readout Acquiring images Acquiring images Background information opens the dialog box containing the slide control for the sharpen filter Maximum values are 30 soft and 30 sharp The value 0 makes the filter have no effect activates deactivates the automatic contrast enhancement Now the image will al ways be shown with enhanced contrast onscreen no matter what the actual illumi nation conditions are All of the pixels are used for calculating the current histogram This histogram is evaluated for the automatic contrast enhancement In addition the histogram determines the automatic exposure time which you can access by clicking the Auto button located in the camera controls Only pixels of a horizontal and vertical line each one pixel in diameter located in the center of the image are included in the histogram s calculation Only the pixels within a frame set by you Region Of Interest are included in the calculation of the current histogram sets a red frame into the image which you position with the mouse and whose size you can increase or decrease by keeping your left mouse button depressed The right mouse button enables you to set the frame which then becomes invisible activates deactivates the fixed scaling contrast enhancement It works with fixed limits unlike the automatic contrast
19. The blue line must be the exact same length as the cali bration length you entered 16 Click on the Save button to open a list of calibration data for various magnifi cations The magnification table Magnification Table EZ is where you check your calibration data The di Magnification Pixel width Pivel height agram shows the recip umi urri rocal pixel size versus To PEER ia TWIT magnification The SO 00000 D a333 D a3 20 00000 0 83472 0 83472 ade et 10 00000 1 65289 1 65289 along one Ine 5 00000 3 35570 3 35570 You may also set the magnification of an input Delete All channel toa value that Errand E is not in the magnifica a Help tion table To do so use a the Set Magnification command Interpolation is then used Magnification 17 Select any value in the Magnification Table dialog box and click the Delete All button should there be any invalid calibration data in the list when beginning 18 Then click the Add button to add the data of the calibration you have just com pleted to the magnification list and have it included in the diagram as well 19 Exit this dialog box by clicking on OK Acquiring images Saving images Background information 20 Now set your microscope to the next magnification level 21 Repeat steps 6 through 16 for all other magnifications The last calibration should thus be conducted at the greatest magnification level 22 Confirm your input calibration by cl
20. To do this you first click the Select Page Template button and save the page template via the Save Page Template button under a different name In order to delete a page template from a report template open the report template and have the list of current page templates displayed The Delete button is located in the Select Page Template dialog box Page templates are defined within report templates You can however also create new page templates within a report or alter existing ones To do this simply click the buttons of the Report button bar shown on the left Please note that any changes you make to a page template within a report only apply to that report The report template that the report is based on remains unaffected The next time you create a report using this report template you ll have the same un changed page templates Creating a new report template You can only create a new report template based on an existing report template If you haven t created any of your own report templates yet then go to the General tab where you ll find predefined report templates that are included in the installation and which you can modify for your own purposes 1 Select the File gt Report gt New command gt The New Report dialog box offers you all report templates that are located in the current report user template and workgroup template directories 2 Select the report template in the New Report dialog box you wish t
21. base field s properties gt The name ofthe new database field will be entered in the Field name field User field consecutive number will be proposed Archiving Images Define organizational fields Step by step 3 Change the standard name of the new user field in the Field name Enter for example Customer as the new user field 4 The Data type list offers various types of data Select the Text entry 5 Mark the Required check box In this way the customer must always be entered when a new project is set up With this step you 6 Mark the Organizational field check box This means that the information decide that the new regarding the customer belongs to all records which are stored under a project M o 7 Close the Add Field dialog box by clicking OK l gt The new database field has then been set up and will be displayed in the Available Fields list gA gt All of the database fields are characterized by an icon in the Define Fields dialog box The new database field will be prefixed by the icon for a user defined organizational field 8 In the Default group select the option next to the empty editing field Thus when a new project is set up the Customer field is always free and must be re entered explicitly 9 In the Picklist group click on the Edit button to set up a selection list for the Customer field 10 In the Edit Picklist dialog box enter the name of a possible customer into the Value field e g
22. look for an appropriate image structure and focus it Click the Snapshot button to acquire an image e You can also measure directly in the live image To do this however the live overlay must be activated To do this mark the Live overlay check box located in the Image gt Configure Input gt Display tab The overlay can become rather confusing if you measure many values in the live image Click the button with the eraser symbol located on the stan dard button bar to delete the overlay The already measured values will not be deleted in doing so 5 Measure the desired segments 6 Repeat the last two steps for all the images on which you would like to make measurements gt A new entry for each image is automatically created in the measurement display As soon as you begin a measurement on a new image all of the already existing measurements are reduced to the main entry in the tree view Interactive Image Measurement Using Statistics Functions Background information Using Statistics Functions Background information Statistic display S A total of 60 segments were measured on nu merous images The mean segment length is provided The spread of the measurement re sults is provided by the standard deviation Select parameter Create sheet Step by step Your image analysis program automatically creates statistics for each interactive measurement which are shown in the Statistics group located in the measure
23. 5 Click the Zoom In button to double the current zoom factor gt The test image will now be displayed at a zoom factor of 60 6 Click the Adjust Zoom button to have the zoom factor adjusted to fit current viewport size e The length width ratio of the image will not change Unlike the automatic zoom factor this zoom factor is not linked to the size of a window i e even when you adjust the size of a window the zoom factor stays the same 7 Alter the size of the image window 8 Click the Adjust Window button to have window size adjusted to fit current im age size 9 Click the Zoom button in the viewport manager gt You will now see a magnifying glass appear in the active viewport Use the mouse to move it As soon as the magnifying glass touches the top border of the viewport the image will be moved upward First Steps Saving GUI configuration Background information e Leftclick to raise the zoom factor by 100 e g from 300 to 400 Rightclick to lower the zoom factor by 100 e g from 300 to 200 The minimum zoom factor is 100 Click the middle mouse button or press Esc to exit the zoom mode 10 Click the Select Viewport Manager Pane button located in the viewport manag er Select the Navigator view Select what image segment you want shown in the image window within the thumbnail e Move the mouse onto the red frame border around the thumbnail The li mouse pointer will change shape turning into a d
24. 505 81 4101 55 45 02 1709 48 23 30 2820 19 1704 25 23 23 083 42 4543 61 24 11 4158 80 584 19 527 25 12 568 3164 32 29 60 2026 90 4182 45 16 31 1061 74 14 52 1607 87 24 99 3821 73 52 27 819 68 11 24 4232 12 16 85 1670 06 27 84 2581 80 827 03 11 31 590 00 43 54 1972 77 26 98 30147 28 41 27 4320 97 48 20 085 87 3015 16 27 56 3244 45 1065 55 44 57 4131 16 415 47 165232 22 60 2841 67 38 87 1605 87 23 06 512 90 2017 42 27 59 2737 93 1642 77 22 47 884 90 42 10 1583 03 24 65 23904 83 53 44 o38 26 12 83 422806 16 80 1718 84 23 54 2478 83 47 58 885 29 142 11 14192 45 16 34 4726 90 23 62 104 38 56 14 28720 3 93 850 13 44 63 2409 67 32 96 2568 51 35 43 4462 71 20 28 12 83 4957 00 26 78 2756 25 37 70 1661 48 22 59 AD Plraze Arenlpsix Le Phase 1 0 42 mF WLU 300 J 15 0 3 all Sumner of Y easnuremernrs Inserting sheets into an empty sheet object 1 Close all loaded sheets Simply use the Window gt Close All command to do so 2 Generate a new report based on the Normal template 3 Select the image object and click the Sheet button located in the Report Objects im button bar and pull open the sheet object 4 Load the sheet you want to insert into a report 5 Select the sheet object on the report page and click the right mouse button 6 Select the Select Sheet command from the context menu to open a list of all the sheets loaded and to insert the desired s
25. Background information Image database An image database enables a structured storing of all your images It enables you to access a great number of images fast and easy Database fields Database fields determine the structure of your database Database fields define the criteria relevant to all information you wish to save along with the images Database field entries provide an unambiguous characterization of each image which allows you to locate each image in the database Archiving Images L L 182 Report Generator Report objects Background information Predefined fields User defined fields Record object Database images from the image man ager What make up record objects Inserting sheets 192 Inserting diagrams 197 Predefined fields are fields prescribed by your image analysis program They contain image data information that your image analysis program can automatically read out e g image calibration The predefined fields of each image database are the same If you only use predefined fields in your reports you will not have to adapt the record objects of your report to your database Set up your own user defined fields for each image database e g user project comment or instrument These fields are usually different for each image data base Record objects that refer to user defined fields can thus only match one par ticular image database You can insert images directly from an
26. Ci The new database called ExpressDatabase01 is ExpressDataba Folder 1 i set up y ExpressDatabase01 apl Field name Field value Ca Folder 1 File Name ExpressD atabaseQ1 Path c V4archive ExpressD atabase01 ExpressD atabase Created 27 02 2007 16 57 06 Last access 27 02 2007 16 57 11 Modified 27 02 2007 16 57 11 Opened exclusively yes Read only no Database identifier 6C5QH8J6 Converted from mdb no Database version 2 03 102 H ExpressDatabasel1 Sel 1 0 kB 6S 60 Archiving Images Define a database Background Information Define organizational fields Background Information Predefined fields User defined database fields Organizational fields Icons for database fields Step by step Predefined fields are provided by your image analysis program and are saved with each record automatically They contain the image attributes and data which the system assigns on input into the database They cannot be edited or deleted An exception is the Record name field the entries in which you can edit while inserting images or editing record names unless you have determined something else in the Database gt Administration gt Settings dialog box User defined database fields can be set up according to your requirements e g User Project Comment or Instrument You can define the data type of the entry for each field You can also define whether during the in
27. Database gt Open menu command or through the file list at the end of the database menu Open the database To open a database exclusively use the menu command to open the database and exclusively mark the Exclusive check box in the Open Database dialog box If you mark the uppermost entry in the tree structure you will see whether a database has been opened exclusively You must open the database exclusively if you want to carry out operations which could alter the structure of a database e g e defining or editing fields e deleting the database e defining a database password e changing image and document paths e changing the standard image format Datatypes You can select different data formats for database fields e Text letters and numbers up to a maximum of 255 characters e Long whole numbers e g 10 O or 500 e Decimal number whole numbers and fractions e g 1 2 whether a comma or a period is used for decimal fractions depends on the local settings of your oper ating system e Date Time The permitted date and time formats depend on the local settings of your operating system e Memo any length texts e Yes No For fields of this data type there is either the status Yes or No A check box appears during insertion and editing of the record Step by step Defining the database fields for the characterization of individual records A database should contain the field method of investigation For every record
28. Define a database Set up a new database Term definition STAR STructured The STAR database is integrated into your image analysis program It allows the ARchive structured storage of all of your images graphs and documents such as sheets diagrams and text You have fast and easy access to even very large amounts of data all the times The database has full network capability and can be accessed by several users simultaneously Step by step Defining the directories for data storage 1 Select the Special gt Preferences command 2 Click on the Database tab 3 In the Locations group select a directory for the storage of all database files If several users are to access the database select a network drive which can be accessed by all users 4 In the Locations group select a Temporary storage directory This directory is used as temporary storage for files during data saving and archive work in the database 5 Check the preset backup volume capacity for the backing up of your database You can change this setting later when making the backup copy e Ifyou store your database on CDs enter the volume of the data carrier into the Backup volume capacity field in MB e g 600 e If your network database is backed up by the system administrator enter the value 0 into the Backup volume capacity field 6 Close the Preferences dialog box by clicking OK Term definition Organizational ID All data is entered into a data
29. Diagramt File name Nagrand st Skip N Type Diagram Gilent Selection index 2rd Cancel Help The list contains all of the loaded documents Databasell apl Froject 2 Database apl Diagram std Field value Fy Project No Project 2 kd Se 1 OkB 4 Databasel Project 2 GZ 76 Archiving Images Work in the database window Background Information Work in the database window Arrange Fields Background Information Image data type Graph data type Data data type Step by step All images which have been loaded into the image manager represent a data type of their own This means that you can define special database fields for images e g the Microscope type database field These database fields contain information about the images and can also be used for search purposes For example you could find all of the light microscopic images in the database For some program versions the image manager provides a third tab which contains storage for graphs Graphs are measurement curves which are displayed in a sepa rate document window In the same way as for images you can create database field especially for graphs You insert graphs into the database from the image manager using drag amp drop Remember that you can insert graphs as records by drag amp drop from the image manager and also as documents Database gt Insert gt Docu ments You sh
30. File gt Report gt New command gt The New Report dialog box offers you report templates that you can base your new report on 2 Select the report template named Normal in the General tab in order to create an empty report 3 The Report option is default in the Create new group 4 Confirm via OK to have the report generated gt The first page of the new report will appear within a separate window The first page s appearance is determined in the report template gt Your image analysis program will display a number of button bars to be used in making and editing reports These button bars are context sensi tive i e as soon as you activate another document the report button bars will disappear Adding pages to a report gt The Add Page dialog box will be opened This is where you determine 5 Click the Add Page button in the Report button bar to add a page to the report where you want to add a page within the report 6 Select the Insert page option within the Add Page dialog box to insert the new page directly before the current report page This is the option you choose if you have to add a page to a report that is finished otherwise Select the Append page option to add a last page to a report no matter which report page is the active one or not 7 Confirm by clicking OK gt The Add Page Template dialog box is opened if the used report template contains more than one page template You ll find all templat
31. Grid and Ruler groups You can open this dialog box by rightclicking on any part of a report on which no ob ject has been placed and selecting the Properties command from the context menu The file formats SRD and SRC are available for saving reports Both formats are ex clusive file formats of your image analysis program and cannot be opened with other application programs Select the SRC file type to place all files which belong to the report in a single con tainer file If you insert a report in an image database the report is automatically in serted in SRC format When using the SRD file type the report is not saved in a single file Similarly to the saving of a database there are several files and directories involved Any files that are part of a report will be automatically placed in a subdirectory named after the re port When making backup copies the easiest thing to do is to copy the whole report directory Report Generator Creating reports Step by step Step by step Set report properties 1 Leftclick anywhere within the report on the background gt Now none of the report objects is selected 2 Rightclick and select the Properties command 3 Select the desired properties for the report e g page format For example clear the Snap to grid check box to be able to position all objects as desired via mouse 4 Close the Report Properties dialog box via OK Generating a new report 1 Select the
32. If you click the button and select the burner via Select Directory you will get an error message File Storage x Please choose the destination drive For the storage E E PLEXTOR CD R PX 32014 M Drive type COIOYD In order to store your data properly you need to specify the destination volume size For CD ROM and removable drives Volume size 703 5 MB Auto detect Burning options Burning speed 20 x lt Back Cancel Help 8 Click the Auto detect button to automatically detect the size of the destination drive gt The available burning speeds will be selected together with the size of the destination drive 9 For security reasons do not select the maximum burning speed but stay one level below it This reduces the possibility of errors 10 Click the Next gt button 11 Select the scope the backup is to have Select the incremental backup option for example e Please note You can save all the database files or only those which have been altered since the last backup If you save all the database files the files with the APL MTB and TNB file name extensions are always written to an individual CD DVD If you only save altered database files clear the include database files check box to abstain from saving the database files Then you should save the database files in another manner 12 Click the Next gt button gt The system now calculates the number of data media required 13
33. Info 11 T Table View Database 79 Temporary storage directory Database 89 Test image 19 Texture images 128 V Viewport 18 Viewport Manager Magnifier 124 Navigator 124 Viewport manager 12 W White balance 34 60g 210 Index intX 26 Workspace 21 Loading workspace 24 To create a workspace 23 X XY Calibration 37 Z Zoom 18
34. OF Cancel Help Perhaps you are only interested in large and bright particles or only particles that have at least one hole Particle filters enable you to use particle parameters for excluding certain particles You define a range for each parameter Any par ticles that are not within the range defined will not be taken into account in the evaluation sheet Border particles are particles that are not entirely within the detection area There are four ways to treat these particles e Truncate the particle is clipped by the search area frame ROI or mask being detected Border particles can be treated in different ways dur ing particle detection All four of these options for dealing with border particles are only available when de tecting via frames The Include 50 option is not available for detection via ROI Border particles are always clipped when detecting via mask Pixel connectivity left Pixel connectivity de fines which pixels are con sidered part of a particle right Holes within particles can also be analyzed in clude the holes in your de tection and use the hole par ticle parameters Hole Count and Hole Area Holes Step by step Image Analysis Defining detection Step by step e Include the particle as a whole will be counted in the detection process if partially clipped by the frame or ROI e Include 50 the only particles counted during detection are those in con tact wi
35. OK gt You will be returned to the Save Image As dialog box gt The Compression field shows the current compression method 9 Click the Save button gt The image will be saved at the path selected Deleting images in image buffers i e the image manager 1 Select the Image gt Delete Image command to delete the image from its image buffer gt The image is simply removed from the image buffer The actual image your have saved is not affected by this command e You can also throw out an image by simply dragging amp dropping it onto the recycle bin icon in the lower part of the image manager or just press Del to delete an image in the image buffer Use the icon area of the age 23 image manager for 23 55 x 383x8 quick and easy drag amp drop access to basic operations such AA Q gZ as deleting saving Lo is printing and database _ T Kr insertion Recycle Bin Save Print Database Icons Printing images Background Information Print Templates You can determine the print template for different document types To do so use the File gt Define Page Layout command The template contains the page layout of e single images e multiple images e database images and e other documents e g sheets and diagrams A page layout consists of header footer definition and the position and magnification of images The report generator gives you many more possibilities as well as very complex pa
36. Production 11 Click the Add button to take over the entry from the Value field into the picklist e Check the entries carefully Typing errors can only be corrected with great difficulty at a later date 12 Confirm the picklist by clicking OK to return to the Define Fields dialog box gt The Picklist group in the Define Fields dialog box can now be accessed 13 Select the Restrict input to picklist entries option so that only the given customer can be accepted when creating a new project 14 Repeat the procedure from step 2 to define further organizational fields such as for example approved by or estimated completion time 15 Inthe Define Fields dialog box click the Close button to complete the definition of database fields L9 62 Archiving Images Define a database Step by step How to define organizational fields Organizational ID Define Fi Ids x ie Eas ies z Nami woject No Ten e wo ane Data type 7 Input requi Edit amp paucio File sary All Ets ior bees Picklist predefined E Calibration Unit gt E Channel E oo database sack weds T Don t expant f ty Document Creation Date fields Document Creation Time i Expand pichist a locument Files Size a piei Restrict input bo picKINMentries EYDo icument Insertion Date Epc cument Insertion Time Batumis CUS aT tr Add New Field B EpDo ocument Modification Da Field properties
37. a database the Insert Images dialog box is opened List of all loaded images Insert Images The selected images in the image manager have already been selected x 1 Yeast DLE comected_ uh 2 MlA 545 Human Brain 3 Renal 4 Adenovirus Overview 5 Immunogold Threshold 6 Immunogold analysis Immunogold Separator Select All Unselect All Help OOOO K K The insert mask for inserting an image The record name can be issued automatically Insert Image Fields 1 4 Record Name Client Preparation Thumbnail Observation Method Database fields with information about the image fet Database _apl El t 0 CSB Elev e a 4 28 i ele 3 UMA a EF roject 2 Project Mo Project 2 i Yeast_DCE_core Fixed no The images are inserted ie ig Human B Tine a at into the project file Parsee e a ja k Client o do 4 F Databaseli Project 2 Sek 1 0 kE 2 Archiving Images Inserting documents Background Information Inserting documents Background Information Documents Documenis include all those texts diagrams sheets and reports which are loaded in your image analysis program You can insert documents directly into a database folder or also into another image or data type record Differences Differences between documents and records of the image graph and data type e No
38. all the images you want to measure 2 Click the Switch context button in the standard button bar gt The image window is automatically maximized gt All but one of the button bars are hiden gt The buttons for image acquisition are additionally integrated in the image window s button bar gt The Switch context button bar appears on the left side Baton eseriton Close Switch Ends the Full Screen mode The user interface once again context looks like it did at the beginning of the Full Screen mode Select previous Activates the next image buffer respectively the previous im buffer age buffer Select document Opens a list with all open windows image window database a graph window 3D window sheets and diagrams Display addi Opens a list with additional components which can be added tional compo in Full Screen mode standard button bar image manager nents and viewport manager 3 Click in the image window s button bar using the right mouse button gt A list with all the available button bars appears 4 Select the measurement button bar from the list 5 Pull the button bar to a preferred position e g under the Switch context button bar 6 Execute the measurement on the first image 7 Click the Select next buffer button to display the image in the next image buffer and to measure it 8 Exit the Full Screen mode after the measurement in order to exit and save the measureme
39. analysis program offers you an entire row of measurement parameters from which you can choose the appropriate one Even after the definition of the measurement object you can always alter the measurement parameters which are to be exported Various measurement parameters are only available for various classes of measure ment objects The measurement of the area of a line is senseless and therefore is not even offered as a function when measuring line objects The selected measurement parameters are shown in the tree view in the Measure ment tab as well as in the measurement sheet You will find a description of all the measurement parameters in the Select Measure ments dialog box In the measurement parameter list click on the name of a param eter to show the description and a schematic drawing in the dialog box You can print a list of all the measurement parameters from the online help The Radius Mean parameter is explained here as an example The radius mean of an object with any form e g rectangle is calculated in the follow ing way the program calculates the center of the object and lays many straight lines through this point Two intersections of one line with the actual perimeter deliver the values for a radius The mean radius is the mean value of all radii determined this way The mean radius is the circle s radius when dealing with a circle The Select Measure ments dialog box is di vided into numerous sections 1 You
40. apply the Contrast or Histocontrast filters You set image contrast yourself when us ing these 9 Apply other filters until you have altered the image as desired 10 Click on OK to have the resulting image written into the destination image buffer gt The preview window and dialog box will be closed gt The resulting image will be shown in the active viewport E FIS 1 iol x Apply Filters Ed Filter List Intensity Feecute Contrast Histo Contrast nee Sharpen Remove Moize E Reinitialize File Help 0 1 100 0 i Interactive Image Measurement Interactive Image Measurement Background information Interactive Image Measurement Your image analysis program offers a wide range of measurement functions They enable you to quickly count objects and measure segments areas and angles All the results are saved together with the images and can also be exported to a sheet Background information Measure ment Envi ronment The measurement but ton located in the stan dard button bar acti vates or deactivates the measurement environ ment All the measurement functions can be found on the measurement button bar Simply be gin a measurement by clicking on the appropri ate button The measurement dis play which contains all of the measured values is activated in the image manager Exporting measure ment results The measurement environment is a user
41. calibrated image intensities palette bars show how gray val ues and image intensity values correspond right The above ex ample shows a height map as it is generated by e g the Stereo add in Acquiring images Showing scale bars Step by step e Select the Adjust to printer frame check box if you wish to export images and automatic scale bar into another application program e g MS Word via the clipboard Scale bar size will be adjusted to actual print size of the image This of course requires that subsequent print size be known and is entered correctly e Select font size for printing out copying into the clipboard and burning the scale bar into the image in the Clipboard Burn image group e Enter select the font size desired for labeling all scale bars into the Font size field The font size selected here does not affect onscreen display of scale bars 5 Confirm by clicking OK e All scale bar settings are global settings i e they apply to all loaded im ages 1 Reference Image 100 4 18 Height Map 90 D B T ac LV 48 Saving Printing E mailing Saving Printing E mailing Background Information Saving Printing E mailing Saving images Background Information Saving images Image file formats Your image analysis program supports nu merous image formats ranging from the most common to more spe cialized formats used by certain systems for im age generation Image
42. click the lt lt Remove button Close the dialog box by clicking OK gt The minimal and maximum values have disappeared from the measure ment display 5 Click the Create Measurement Sheet button located in the measurement button bar 6 Mark the Generate statistics of the sheet s check box located in the Create Measurement Sheet dialog box and confirm with OK gt A sheet with the statistic parameters is created and shown in addition to the measurement sheet All of the measured values are acquired to the sheet A separate column is created for each value The statistic parame ters shown correspond to the parameters which you selected in the Define Statistics dialog box i Measurements of Image Miel Ea 20 Object 20 Object ect 20 Oneri _ Statistical Function 2D Object 2D Object pi Are Perimeter Base Unit pm pm mm 7983 72 4492 64 3718 14 1AA Aad 3677 28 standard Deviation 195110 01 05 A Measuring Arbitrary Structures Background information Magic wand H Use the magic wand located in the measurement button bar to quickly and comfort ably select an object of any shape To do this you mark a a typical point within the object Your image analysis program then automatically searches for points in the area which have similar gray or color values An object which can be collected with a magic wand must be able to differentiate itself from the background based on its color or its gray value
43. color components of one of the color models into true color images define overlay objects of any shape and color clip fill and copy image areas of any shape Applying multiple When working with the RGB Studio multiple filter operations can be executed suc filters cessively without having to select the RGB Studio gt Apply Filters command each time Each operation is applied to the resulting image of the previous operation and then placed in a stack This stack consists of all the filter operations in their order of Processing images Filtering RGB images Step by step application on the image This stack processing is reversible i e one or more image operations can be reversed successively at any time if you re not happy with the re sults and thus wish to apply other filter operations modifies pixel intensity values via the gamma function Non linearities of camera and monitor can thus be corrected Hue modifies the pixel colorvalueH o Saturation modifies the pixel saturation value S S trast histogram to adjust image contrast Sharpen increases or lessens image sharpness O Z o O o Remove substitutes the central color of neighboring pixels for the color value of each Noise pixel substitutes the average color of neighboring pixels for the color value of each pixel an imitation of the effect on photographic film when coincidentally exposed to light briefly Oilify gives an image the appearance of an
44. command gt All current logical input channels are listed in the Set Input dialog box You may duplicate an existing channel and then modify it or set up an entirely new input channel 2 Click the New Channel button gt The Select Device dialog box will be opened You will find predefined inputs for all image signals which can currently be read with your image analysis program 3 Select the device desired in the Available devices list e To display all inputs available click on the plus sign within the tree control E directory Re 28 Acquiring images Configuring inputs Step by step Two different system mses a eer the ColorView Illu Col Available devices or and Black White In E ay S15 View Firewire Camera eee order to be able to use Of BEE Cancel the Black White mode i r e o E Colorview Ilu PY Bw 22610616 you must create a new Help channel Use calibration of active channel 4 Select for example ColorView Illu FW if you have installed a CCD color camera of the ColorView u type The abbreviation FW stands for FireWire e Two channels will be automatically set up for ColorView and ColorView u The channel with the additional BW must be used for the camera s black amp white mode 5 Click on OK gt Anew logical input will be added to the list of available input channels 6 Click the Configure Input button to define the properties of this input channel 7 C
45. directory of your program contains the Images sub directory A selection of TIF images is available here 6 Click the Preview button to view thumbnails of image files Select the image files one at a time 7 Select the images you wish to load First Steps Loading images Step by step 8 Click the Open button to load the images selected gt The Open Image dialog box will be closed gt The images will be loaded into successive image buffers The first image will be loaded into the active image buffer e g 5 The next images you load are then put into image buffers 6 9 if you have loaded altogether 5 images simultaneously Activate image window Sometimes the image window is covered by another window This is the case if a document window has been maximized or if many other documents are open The following step by step instruction is only one possibility to bring the image window back to the foreground 1 Select the Window gt Document Manager command or use the Alt 3 key stroke gt You will find all of the open document windows listed in the document man ager The document type and the title of the document window are given for each document 2 Select the image window gt There is always one image window 3 Click the Activate button located in the document manager gt The image window is now in the foreground Loading images into specific image buffers 1 Click the Gallery tab in the image manager
46. drive from the list Then click the Auto detect button to automatically select the size of the destination drive 8 Click the Next gt button 9 You will get a list of all of the database folders of the database which have not yet been archived or which have been altered after the last archiving Select all the database folders which you would like to archive These should be finished procedures To do so use the operating systems default key stroke Ctrl key left mouse button selects single records Shift key left mouse button selects a row of records Ctrl A selects all of the records Click the Next gt button 10 Before starting archiving carefully check the data in the File Storage dialog box 11 Click the Finish button to begin archiving 12 Follow the instructions of the database wizard gt After successful archiving all of the archived records are marked by a lock in the database window The table shows icons used to identify records within the database window s tree structure read only record f _J No data can be inserted into this folder 3 5 archived record amp Le Additional data can still be inserted underneath this record archived and read only record No additional data can be inserted into this folder The folder was locked during archiving 6 94 Archiving Images Protect with a password Background Information Protect with a password Background Information D
47. ee eS Erki i Erka by Erlise agree ap Size 2 2 alr SA Query results on 16 Bit Display Mag E gt Ca 2D Surface a at A GACT yy ty Gy ADDA AOTEA Ca Analysis Sintered Mate Qj Automater Da Calibration yj Caston CQ Chain yj Colo Adjustment Lg Color Separation Ca Color Threshold yj Database Ca EF Cy FFT Cy Filter CQ Grains CQ Graph Processing O Image Acquisition Ca Layer Thickness M Po Memeo color filter LeamSiS YADDA A Fruty Adapting record objects to your own database Your image database generally contains fields that differ from the sample templates included You have defined e g the Material or Order number field in the data base and in this case you want to have this information included with each image In this case you ll have to adapt the record objects to your database Adapting record objects to your own database is usually carried out by a report tem plate Only then are newly defined record objects which are based on this template available 1 Select the File gt Report gt New command 2 Select the Normal report template in the General tab Select the Template op tion in the Create new group 3 Confirm by clicking OK gt Your image analysis program creates a new report template The header of the window displays the name of the new report template Template1 and the name of the active page template 3 image pag
48. field What you are doing now is simply defining the layout You can then later on apply this layout to any database field you like gt No object templates have been defined for the Normal template which means that the standard field object will be automatically inserted If you have already defined object templates for fields the Select Field dialog box will be opened al 5 Click the Edit Object Template button in the report window button bar to switch 2 over to the object template editing mode in this case for the field object e Please note that you are already in the object template editing mode You can edit object templates in several multi level steps Now define a field ob ject template gt You can now select the separate elements of the field object and then edit them gt All other objects even those of the active record object will only be shown for reference purposes and thus appear crosshatched These can no long er be selected 6 Now you edit the field object e The field name is an essential part of the field object You can omit the field name when defining an object template for a field object but you cannot replace it with a fixed text aa 7 Click the Finish Object Editing button to save the object template for the field a T object 8 Enter a relevant name for this field object into the Finish Object Editing dialog box and click the Save Object Template button gt This will return you to the record
49. from the image manager onto the gallery view in the database window The images will be inserted at the same level as the thumbnails that are on display No records can be inserted immediately below the first level In this case you will receive a message and you can set up a new database folder The images will be inserted one level below the thumbnails that are on display You cannot insert any data here That is for example the case when six levels already exist below the database folder Additional data cannot be inserted under a document Insert An image can be inserted into the database directly after the image acquisition To Snapshot do this select the Special gt Preferences command On the Image tab select the Database entry from the Image acquisition gt Sequence list Before you switch into live mode mark the database folder to which the image belongs in the database During the image acquisition the image will be automati cally inserted into the database 69 70 Archiving Images Insert data Step by step Step by step Inserting images from the image buffer box The step by step instructions assumes the following prerequisites You have created a project database The database already contains a database folder You have acquired images for this project which are to be filed in the database below the data base folder 1 Mark the project in the tree structure which you want to use for filing the images
50. full images Select either a high resolution im age display or thumbnail This selection only affects the display of an im age on the monitor and not the image quality in the actual printout 4 Click OK to close the dialog box 5 Generate a new report based on the Normal template 6 Insert at least one image object To do so click the Image button located in the Report Objects button bar 7 Pull an image via drag amp drop right out of the image manager onto the image ob ject within the report gt The image will be inserted into the report and shown in the report window Image Manager E Al Reporti n Cn TEF Se Je Dea E Mal Liver Tissuel 1 E 867x731 x16 EFI Cryste 2 a 730 572 24 Br i 730 572x8 Pyramid i 1254 990 24 Microhardness 5 EL 1260 102424 Ge Jeti 6 a 600x600x8 Jet4 7 Ll bo0xco0x8 E E Fruitfly 8 2048 x 2048 x8 Sintered Matena 9 bax aaas 3 color filter 10 fo x blOx 24 w Catalyst ii 1280 x 1024 x 24 21 0P ae Pa i oof d E Postion 0 00 0 mn Ses 217 6Z1 180 Report Generator Report objects Step by step Changing the print size of an image 1 In order to display an image at a different magnification level select the image object by leftclicking on it 2 Click the Properties button in the Report Objects button bar to alter any of sev eral image object properties especially print size 3 Click the Imag
51. gt In the database window you will find a preview window The preview window shows the record which is marked in the tree structure If a data base folder is marked then a folder icon is displayed 2 Mark all the images in the image buffer box that you want to insert e You mark a linked image buffer area by depressing the shift key and clicking on the first and last image e You can mark a random selection of images by depressing the Ctrl key and clicking on the images you require 3 You can use drag amp drop to move the images from the image buffer box to for example the preview window of the project Select all the images in the image buffer box kumia 4 eanne nearer ee By depressing the left Sic Fe Dest Sree Mask mouse button you can drag the images to the positions 1 2 or 3 of your database window No records ayvailat S Froject g Field value Project Ho Project 2 Fined Ho Time 16 23 Date 27 02 2007 Client U4 5 Zinnkugeln 1 Databasell Project 2 EE List Lal Gall E 4 When using numerous images the Insert Images dialog box is opened go to illustration on the following page gt The check boxes in front of the selected images are marked You can still change your selection at this point e f you only insert one single image into the database the insertion mask will open directly 5 In the Prompt for data input group select the Always option 6 Confirm the im
52. has two advantages for the sending of reports you can considerably reduce the report s file size and the recipient can open the RTF file report in other applica tion programs e g MS Word Step by step Saving Printing E mailing E mailing images Step by step Send email Preferences x Image Report Other Documents General Image format Compression Mone OK Cancel Send email Preferences Ea Image Report Other Documents General Reduce image data Export images as thumbnails I Set image resolution 75 DPI W Use JPEG compression 75 How to e mail Options Hel Save Image Options Ea TIFF Preprocessing tomer G bit mages to ahit T Burn overlay into image Compression F Quality es B Choose format Send report az a report container src stc Send report in Rich Text Format rtf OF Cancel Help 1 Open all the documents and images you wish to send in an e mail e If you re planning on sending database images and documents open the database s and select the records desired 2 Click the Send emai button in the Standard button bar Or select the File gt Send email command gt The Send email dialog box lists all images and documents currently load ed open in your image analysis program e All the files in this document list are selected by default Saving Printing E mailing E mailing images Ste
53. image win dow is divided up into several windows i e viewports Each viewport can display a single image To alter image display within the image window e g zoom factor use the Image button bar Status bar The status bar displays the following and more e brief descriptions of all functions Simply move the pointer over the command or button for this information e name ofthe active input channel e position and size of the global frame Loading images Background information Loading images You can load several images simultaneously Click the Open button in the Open Im age dialog box to load all selected image files The image files will be loaded into suc cessive image buffers The first image buffer is the active image buffer To select e a continuous group of images Leftclick on the first of the images Then while pressing Shift leftclick on the last one of the images Image buffer box icons A resolution of 318 x 223 x 24 corresponds to a true color image with a bit depth of 24 width of 318 pixels and a height of 223 pixels The gallery view shows you thumbnails in the image buffer box of all images currently loaded right First Steps Loading images Background information e anon continuous group of images Select the first image by clicking on it with the left mouse button Keep the Ctrl key depressed as you select all image files needed with the left mouse button e all images within a dir
54. in the active image buffer will always be displayed in the image win dow independent of how many other images are being displayed e The active image buffer contains either the live image or an acquired image Any interactive input or measurements are always applied to the active image buffer Commands you use frequently are linked to a button providing you with quick and easy access to these functions Please note that there are many functions which are only accessible via a button bar e g the functions required for editing an image overlay Use the Special gt Edit Button Bars command to make button bars look and include what you want them to The viewport manager enables you to determine how images are displayed in the im age window Your are provided with many ways no matter what the application for displaying your images optimally onscreen You can hide the viewport manager to create more room for other windows for example To do so use the Alt 1 key stroke The image manager contains numerous tabs Click the different tabs to alter the ap pearance of the image manager The first two tabs List and Gallery are reserved for the administration of images The operands box is for e determining source and destination image buffers used in image processing op erations which alter the original image e g inversion e linking images for certain image processing operations e g addition of two im ages Use the image buffer bo
55. in the tree structure gt The preview window shows the thumbnail of the selected image gt The gallery shows all the records which are behind the image gt The form contains information about the selected image L8 Archiving Images Work in the database window Step by step How to sort your records Click this button to display the data ina different order The record name is the current sort criterion Sort by Record Hame T Calibration Unit Camera Length Channel Comment Device Type Document Creation Date Document Creation Time Document Files Size Document Insertion Date Then by not specified 82 The date created is the new sort criterion for the folder The folder entitled lt New Folder gt has just been newly set up This is the reason why it is still empty and appears at the top of the list amp iTEM apl Ss 0 lm elf ya General Gain correction cu ITEM apl H CA BioMedical science General Ascending Descending Aerenoing Descending Ascending Descending a Ascending Descending iNew Folder Mo records awallable i New Folders W gy aea ence H C3 BioMedical science H CA General ITEM lt New Folder A Archiving Images Choose View Step by step Step by step Changing the view of your database 1 Select the Database gt View gt Choose View command gt The Choose Vi
56. interface which has been optimized for measurements done on an image This measurement environment enables quick ac cess to all measurement functions measurement results and settings which effect the measurement Measurement Measurement Measurement display button bar button 2 analy5 File Edt PP atabave ane li Hesu Anal Graph 30 Chode Special Window T H 1 Elipscide EB Pa Origin m 0 20 Objed Area 5353 95 pr Peimeter 277 55 um Radus Mean 47 55 eu Ubed Area 6501 77 ur FPaineter 309 03 um Radus Meare 46 31 eu Jejeg Apes 5467 37 ur Paameatar 375 57 yum Rode Mean 44 47 a 20 DEEH rea MOLS pr Penmatar 217 UA yr Radus Mear 33 11 20 Object Apes 4912 08 unt Ciunt 3 Hear 4365 ae ee S40 af Ready Sci saz it oo The measured values are displayed in color in the image s overlay In addition all measurement functions create an entry in the measurement display These mea surement results remain linked to the image even after the image has been saved You can export the measurement results to a sheet any time To do so click the Cre ate Measurement Sheet button located in the measurement button bar LLL 112 Interactive Image Measurement Interactive Image Measurement Step by step Measurement All the measurement functions can be found on the Measurements button bar There button bar is one button for each function Begin a measurement by clicking on the button with the de
57. less space is available in the temporary storage directory than defined in the Special gt Preferences gt Database gt Backup volume capacity no more data can be added to the database In this case you will be asked to archive data To do so select the Database gt Administration gt File Storage command Both single images and the entire database can be deleted without too much effort And no storage medium provides 100 data protection For this reason you should protect your database against unauthorized access and data loss as a result of accidental deletion or damage of the data medium e Protect your database with a password 68 90 Archiving Images Archive data Step by step e Make backup copies at regular intervals Backup Security When making a backup or security copy you copy the database data so as to use copy the backup to reconstruct the database in case of data loss A backup copy must therefore be made on a regular basis so that the data is as up to date as possible The original data remains unchanged in the database To make a backup you can either use the software wizard for file storage or the backup software which you normally use to secure data Warning i You should DEFINITELY make backups of your database at regular intervals Select the Database gt Administration gt Restore Database Backup command to use the backup when restoring individual database folders following data loss Database wiz
58. manager and image manager Moving your model 1 If the 3D Navigator is not shown select the Window gt 3D Navigation com mand 2 Click and hold the left mouse button on one of the 3D Navigator buttons to execute a transformation 3 To accelerate the motion click closer to the navigational button s outer edge 4 Ifthe motion seems too slow press the Fast positioning button inwards 3 D button bar upper edge of 3D window gt The model will disappear from view during the actual motion and a visual positioning aid will be shown 6c L Creating 3 D surfaces Editing models Background information A Images of the 3 D model texturized using the intensi ty values of the height map left including the texture image right 130 5 You can press the following to move the model Ctrl arrow keys rotation tilt to the right or left backwards forwards Shift arrow keys l move rightward or leftward upwards downwards Shift PageUp reduce in size or enlarge PageDown Shift Home reset to default position 6 If the model is no longer in view because it is positioned outside of the 3D window doubleclick on the center of the 3D Navigator Model presentation 1 Click the Hide Bottom Grid button inwards 3 D button bar upper edge of 3D window to have the grid disappear 2 Click the Rendering Settings button 3 D button bar Select the Anima tion tab e
59. mm Size 210 0 297 0 mm As Object templates You can create your own templates for records and field objects These templates determine what your record or field objects look like and their make up Object tem plates are saved under a separate name within the active document You can then insert them into a report at any time You define object templates within a report tem plate generally so that you can use them with all the reports you create based on this template It is not possible to import object templates from other report templates Step by step Adding several images from one image database 1 Generate a new report based on the Normal template 2 Open an image database of your choice 3 Arrange your report and database windows such that they re next to each other but not overlapping e To do so use the Window gt Document Manager command Keep the Ctrl key depressed and select the Database and Report documents Click the Tile Vertical button and close the document manager 4 Insert at least one record object To do so click the Record button located in the Report Objects button bar gt The mouse cursor will change its shape Click on the approximate spot N where you want to have the record object placed in the report The position you click on represents the center of the record object You can position VO the record object after editing gt The Select Object Template list will be opened This is where
60. new template page added to the report template gt The new template page called ImageGallery will now also be available to you when you create a new report based on the current report template Saving report templates 1 Press F8 to open the Preferences dialog box and select the Report tab gt You ll find the standard path name for saving reports and report templates in the Directories group gt Your image analysis program will propose the Report directory for saving report templates 2 Enter the path name you want to be using for saving your templates into the User templates field e Ifthe report directory is not yet existent click the button next to the User templates field Click the Create New Folder button in the Select Directory dialog box to set up the directory 3 Confirm the new template path via OK LOZ 202 Report Generator Report templates Background information 4 Click the Save button in the Standard or Report button bars gt When you save a report template for the first time the Save Report Tem plate dialog box will be opened automatically The preset path is the path you entered into the preferences in the Report tab for saving reports 5 Enter a name for your report template that reflects its contents into the File name field 6 Select the report template directory you determined in the Preferences dialog box in the Save in list Warning Your image analysis program will propose the
61. noise increase the value Smooth 7 Select the Burn black option in the Result group to be able to sketch black dividing lines on the original gray value image 8 Click the Execute button to separate particles gt The resulting image in the target image buffer will display the image with the particles outlined in black a gray value of 0 The separating line generated has a width of one pixel e Please keep in mind that the gray value range which defines the par ticles must not contain a gray value of 0 Border Artefacts Image Analysis Setting thresholds Background information Setting thresholds Background information Particle A Particle is a quantity of connected pixels within a defined gray value range This is why you must define a suitable gray or color value range before every particle detection Successful particle detection requires a clear correlation between gray or color values and image structure Analysis button bar The fastest way to access functions for analyzing is using the Analysis button bar To have it displayed just like for any other button bar select the Special gt Edit Button Bars command Then simply select the check box for the Analysis button bar from the button bar list Set Thresholds Define ROIs Define Classification Measurements oo Detection Analysis amp amp Detect Particle Resuts Class Results Frame RO Results thresholds range to define the par
62. object by altering the size of the object Drag e g the lower right hand corner of a text or image object over the upper left hand corner in order to invert the text or image Aligning overlap Objects that overlap each other may partially or completely cover each other up The ping objects object that was inserted last is generally in the foreground You can however later alter the order of the objects Individual objects can then be partially or completely placed in the background You will find the Order OrderandGroup s and Group button bar in AISLE the Button Bars menu 1h 4 Gh WE located in the report window s context menu Step by step Insert report object 1 Load an already existing report or create a new one 2 Click on any position on the report page to activate the report window gt The Report Objects button bar is only displayed if the report window is ac tive You will find the button bar on the right edge of the user interface by default e The first button Select Objects of the Report Objects button bar is engaged by default In this mode you can select and edit as many objects on the report page as you like 3 To draw a new graphic object click the corresponding button in the Report Ob E ject button bar e g the Rectangle button gt Within the report window the mouse cursor will now change shape into a cross shaped symbol indicating that you may now define the object Please note
63. object editing mode eoz 204 Report Generator Planning report templates Step by step 9 10 11 Click the Field button in the Report Objects button bar to insert field objects based on the object template you have just defined Click the Finish Object Editing button to save the now completed record object Use the Record button in the Report Objects button bar to insert the newly defined record object onto a template page Planning report templates Before creating a report template 1 N Using existing templates If it s possible to make use of an existing report tem plate then do it Empty pages mean lots of work as well as the fact that creating so many report elements is redundant Defining your basic layout If possible define all background objects of the report in advance Draft a basic layout including frame s company logo an address space and space for general information such as the department name and or order num ber If you have to make changes later on you ll have to adjust each template page separately Existing reports cannot be automatically altered to fit a new layout This is why any avoidable changes that you have to make later on i e after creating the template take up quite a bit of time Creating a report template involves 1 N UJ Finding a relevant name Give each of your page templates names relevant to their contents This ensures that each user wi
64. or a video camera for ex ample Illustrations and examples in the following chapter are based on the CCD color camera ColorView llu Acquiring images using intX Background information intX Image resolution acquisition and snapshots Camera calibration XY calibration and intX intelligent Exposure of fers a convenient alter native to the acquisition commands Images gt Acquisition and Images gt Snapshot Click the left mouse but ton to start the live im age Click the right mouse button to end the live image and to write the image to the image buffer Calibrating inouts 37 The abbreviation intX stands for intelligent Exposure Use this acquisition process to make good acquisitions with functions that are easy to use The intX acquisition pro cess is only offered for cameras made by Olympus Soft Imaging Solutions A considerable advantage of using intX is that you can select different resolutions for the live image acquisition and for the snapshot A lower image resolution is sug gested by default for the live image since the frame rate is then higher and thus the movements in the live image are not choppy If you are writing a snapshot to the im age buffer it is recommended however to select the highest camera resolution pos sible in order to attain the optimal in image quality intX enables you to automate the acquisition process to a large extent The exposure times for live acquisitions and s
65. report window as positioning aids e Select the object keeping the left mouse button depressed and drag one of the selection markers in the direction desired When simply altering size the po sition of the selection marker opposite the one you have selected will remain un changed e Press the Shift key when you move the corner point of an object via mouse if you want to keep the length width ratio of the object frame the same e Press the Ctrl key to keep the center point constant when altering size of the object frame e Select the object Move the object with the mouse by keeping the left mouse button depressed e You can also select and move more than one object at the same time This means that the objects positions relative to one another remain the same e To move a copy ofthe object and not the object itself press the Ctrl key while moving the object Use the mouse for an initial and approximate positioning of objects Select one or more objects You can pick up the selected object s by leftclicking and then keeping the left mouse button depressed you move the mouse to move the object s to where you wish to have it them Use the grid alignment to be able to position objects fast e Select one or more objects and use the arrow keys on the keyboard to move the object in the direction desired Press the Shift key to increase the distance moved each time you press a key from 0 1 mm to 0 5 mm e Select
66. set from the last detection Check to see if the area to be searched has been correctly defined Select the search area Frame located in the Analysis gt Define Detection tab and deactivate a possible frame The program than detects the particle on the entire image If the Mask option has been selected the particle detection only then offers a result if a masked image exists Select the Pixel connectivity gt Adjacent borders option located in the Anal ysis gt Define Detection gt Detection tab If the particles are separated by lines which are only one pixel in width the Include diagonals option leads to the result that the particles are seen as one even though the border ex ists Select another handling of the border particles For example select the Border particles gt Truncate option located in the Analysis gt Define Detec tion gt Detection tab When using the Exclude option it is possible that no Image Analysis Possible stumbling blocks during a particle analysis Step by step particle will be detected because all of the detected image areas are con nected If the holes within a particle are not filled such an effect is very dif ficult to recognize Classification The detected particles are not sorted together with the defined classifications e Check to see if the current classification scheme uses the correct units If need be define a new classification scheme and use the automatic func tions with which the
67. tabs at the bottom of the image manager If you are offered too many tabs in the image manager do the following hide either the List or the Gallery tabs Use the Special gt Preferences gt Image command Image Manager Ea x be Z ey ET es Image Manager E oppo 1 Water I Poe Origin fo 0 nm O nm 2 Image 2 Length 1 64 pm 2 rel TCO Fpa 0 r m ho Re ee Poi Length 1 35 pm ucan jst Length 1 11 pm im Measurements Click the Create Measurement Sheet located in the measurement button bar to ex port the measured values to a table All measurement values are always exported from one image to one sheet If you have done measurements on numerous images decide whether or not the measurement values for each image are to be exported to individual sheets or if all the measurement values are to be exported to the same sheet The measurement object s type and the measurement values are listed in the mea surement sheet All areas are for example written to one column even if they were defined with different methods If you export the measurement values from numerous images into one sheet the measurements of the same type will be written to one col umn e g all measured areas The unit of the measurement values in the measurement sheet corresponds to the unit in which the image has been calibrated To change this unit use the Image gt Calibrate Image command If you are exporting th
68. the APL file name exten sion gt The form contains the following information about your database The fields shown here are predefined and cannot be edited using the Arrange Fields command Name of the database Complete directory name of the apl database file Created Date and time of creation Last access Last access to the apl database file Modified Last modification of the apl database file Opened Information about the status of the database You can only carry out exclusively operations which modify the structure of the database if the database is opened exclusively Read only Information about the status of the database A database can for example be opened on a read only basis if you have created it ona medium such as a CD ROM Database Clear identification of the database this identifier is only used inter identifier nally Converted from contain the information on whether or not the STAR database was mdb converted from an Archive mdb database Database version Version number with which the STAR database was created 5 Mark the different database folders in the tree structure e g the database folder TEM Acquisition in the example database gt The preview window displays the schematic database folder gt The gallery displays all records which are located one level below the data base folder gt The form contains information about the selected database folder 6 Mark different images
69. the image 2 Doubleclick on the overlay object you wish to edit e Doubleclicking on an object will open the Object Properties dialog box gt The overlay object selected will have selection markers around it 3 Edit the overlay object as desired and click on OK to close the dialog box e The functions offered in the Object Properties dialog box will depend on the object you select Processing images Increasing image contrast Background Information e You can only edit one overlay object at a time i e the Object Properties function is only available when precisely one overlay object has been se lected Increasing image contrast Background Information What is contrast Gray value images have a maximum number of different brightness levels e g 8 bits corresponds to 256 possible gray values In many images however pixel bright ness varies only within a small range i e the actual range of gray values is less than the entire range of available gray values 0 255 Structures in such images are hard to tell apart because image contrast is minimal To optimize the image for the viewer spread the pixels gray values to cover the maximum range thus increasing image contrast What are contrast Contrast operations are where each gray value is transferred to a new gray value via operations a function i e the new gray value assigned a pixel depends singularly on its original gray value Therefore contrast operations are lo
70. the left mouse button Close the area by depressing the right mouse button gt Inthe measurement display you will now find in addition to the measured area the perimeter of the measured object 10 End the area measurement by either depressing the middle mouse button or the Esc key e You can insert additional measurement values onto an image or respec tively delete single measurement values and measure them anew Save Load and Edit Measurement Results Background information Measurement The measurement display is a tab in the image manager and contains all of the mea Display sured values The measurement display is empty as long as no measurement has been undertaken As soon as the first measurement has been started the measure ment display will be filled The values are organized in a tree view The upper most entry contains the number of the image buffer and the name of the image The cur rent position of the image origin is automatically displayed for each image In the tree view the object and the values beneath the object are expanded after measurement A single entry is added to the tree view for each image which contains measurement Origin of the Coordinate System 125 ELL 114 Interactive Image Measurement Save Load and Edit Measurement Results Step by step These images which have been loaded con tain measurement val ues Select the name of an image in the tree view to switch to that image You c
71. the other application program to be able to process the overlay information Please Note Edit Object mode An overlay object must be selected for most overlay operations You can only do this if the mouse pointer is within the image window Click on the white arrow button of the Overlay button bar to get into the edit object mode Delete selections A selection is usually only removed if you explicitly cancel it To cancel all selections you can click on the button with the red X for example Font size You can choose one of two options for dealing with font size in the overlay This set ting is also taken into consideration when printing e You can have your text zoomed along with the image thus ensuring that text size matches image display size If you display the image in the viewport at a lesser zoom level text size will be reduced accordingly The Object Properties gt Text gt Zoom with image check box Is selected in this case e For zoom levels less than 100 you can have the text displayed at a constant size The Object Properties gt Text gt Zoom with image check box is not selected in this case Locked Data Layer The default setting has data layers locked This means that objects in a data layer cannot be selected or edited Overlay Clipboard To copy an overlay use the buttons of the Overlay button bar you cannot use the Windows clipboard Instead of pressing Ctrl c and then Ctrl v you use the but ton
72. to the image window 4 Position the pointer to the starting point of the distance to be measured and de press the left mouse button gt Two edges appear in the image s overlay which are always vertical to the distance to be measured Use the edges as positioning helpers for the dis tance to be measured Interactive Image Measurement Save Load and Edit Measurement Results Background information 5 Position the pointer to the end point of the distance to be measured and depress the left mouse button gt The measured distance is shown in the image overlay gt The measured length is written to the measurement display 6 Repeat the last two steps for all distances to be measured Select the distances you 2 want to measure directly 2 4 min on the image Two edg 5 99 nm i es enable you to exactly a position the start points UWWEEEAWEUET E E e and end points Ay I O79 mm All measurements are x l F E Ei ee a7 mn aed fg min listed in the measure 1 Conducting Paths a a fn mn eee 7 E i 4 mm i 0 0 7 bt 0ra mm Length 33 28 pm m Mouse Pointer 7 You end the distance measurement by either depressing the middle mouse but ton or the Esc key gt The pointer is released 8 Select another measurement from the Measurements button bar Select the Closed Polygon button for example to measure any area with the help of the polyline 9 Set the individual points by depressing
73. to the image window Lol 122 Interactive Image Measurement Measuring Arbitrary Structures Background information The pointer in the left image is located on the object s selected point Only a part of the object is found Keep the left mouse but ton depressed and pull the mouse to the right to select the entire object 6 Click on a typical color value in the object you would like to measure gt The point selected in the object is marked by a blue point in the overlay Your image analysis program immediately looks for the object and high lights it with a red lining in the overlay 7 Should the desired object not have been correctly found keep the left mouse button depressed and pull the mouse to the left to reduce the size of the object Keep the left mouse button depressed and pull the mouse to the right to in crease the size of the object You can view the result as soon as you release the mouse button 8 Click the right mouse button to end the definition of the first objects gt Anew measurement is created in the measurement display The area and perimeter is given as default measurement values gt The pointer remains in the image You can immediately measure additional objects 9 Click the middle mouse button to end the measurement Background information Selecting measure ment parameters Especially for two dimensional objects you can measure a lot more than area and perimeter Your image
74. values are now negative The drawing shows the origin 0 0 and the X 9 9 10 20 and Y directions of the coordinate system You can see the values on the preset Y axis the in verted axis to the right 10 0 0 10 20 Full Screen If you execute many interactive measurements it is advisable to optimize the user Mode interface for the measurement Use the Full Screen mode for example to remove disruptive elements from the user interface and to create as much space for the im age as possible The modus can be activated by clicking the Switch context button located in the standard button bar Click this button to exit the full screen mode To execute a measure ment switch to the Full Screen mode if you need as much room as possible to view the im age Additional acquisition buttons in the image document The measurement but ton bar is not shown in Full Screen mode by de fault You must insert it in order to be able to ex ecute measurements in Full Screen mode Button Bar Interactive Image Measurement Optimizing work environment for measuring Step by step Step by step This is how you measure in Full Screen mode The following step by step How to is only an example of how an interactive mea surement can proceed on numerous images in Full Screen mode You can of course configure the Full Screen mode differently or you can measure in the preset mea surement environment 1 Load
75. where you select a template for a field object Should your report template contain a single format for field objects or not the field object will be automatically inserted in a standard format gt All selected fields are inserted in the record object underneath one anoth er 10 Click the Finish Object Editing button in the report window button bar to save the altered record object 11 Enter a name for the altered record object into the Finish Object Editing dialog box and click the Save Object Template button to terminate adaptation of the record object to your database 12 Use the File gt Report gt New command to save the report templates under an other name 13 Use the File gt Report gt New command to produce reports based on the new ly adapted report template Your own report templates will now be included in the User Templates tab in the New Report dialog box 14 Now insert an image from the database into the adapted record object gt The image and the desired field entries as well will be included in the re port Background information Text objects Text entry mode You cannot enter text into a report directly Before you can insert text you have to reserve space for it The area reserved for text is defined by a text object Text for matting is determined by the text object s properties If you e g use different font sizes in your report you have to define a separate text object for eac
76. within the text object All the lines that do not fit within the text object remain hidden from view This non visible text remains however existent it is simply not shown onscreen You then need to enlarge the text object correspondingly This is why text cannot be any longer than a page Click this button in the Report Objects button bar to insert a text object A new text object automatically contains the word text Keeping the left mouse button depressed draw a rectangle by moving the mouse The area of the rectangle represents the space reserved for text within the report Re lease the left mouse button to have the text object inserted into the document Click the Properties button in the Report Objects button bar to format the text You can also select several text objects and alter all their properties at the same time e Text color is a font property You can set it in the Font tab e Background color is set in the Fill tab The background is the entire area defined by the text object e Use the Line tab to set the frame s properties its width and color You always determine the properties for the whole text within a text object This is why individual words cannot be put in bold or italics If this is what you want then you ll have to compose the expressions using separate text objects Select and group several text objects so that you can alter font properties type size and color background color and text frame for all t
77. wizard s directions Archiving files on CD You have created the database on your local PC You need space on your hard disk and want to export older files from your database System You have access to a CD DVD burner You have Nero Burning ROM software requirements 1 Check the settings for the temporary backup directory Use the Special gt Pref erences command Select the path to which the data is going to be temporarily stored to from the Temporary storage directory field located in the Database tab 2 Check the directory name under which the database files of the database are stored To do this select the upper most entry in the database s tree structure located in the database window The database path is shown in the form in the lower right 3 Close the database from which you want to archive files Make sure that no other user is using the database 4 Use the Database gt Administration gt File Storage command to call up the file storage wizard Archiving Images Archive data Step by step 5 Select the Archiving of Documents option Select the Lock archived records check box In this case you can no longer store any more files in closed database folders after archiving Click the Next gt button 6 Select the database you want to backup To do this enter the path name of the database in the field or click the button to select the directory Click the Next gt button 7 Select your CD DVD
78. you can only display a maximum of seven database fields in the info window e Remember that only one line per field is displayed Database fields of the Memo type are therefore of limited suitability for the info window U1 Close the Arrange Fields dialog box by clicking OK In the gallery view click on the info symbol on the lower right in the thumbnail gt The info window opens It shows your selection of seven fields JH B 7 In the info window click the Keep visible button with a free notice board pin to fix the window on the database document gt The button now shows a sunken notice board pin e Now you can click on any thumbnails in succession in order to look at the selected fields in the info window O 8 Click on the symbol with the cross on the upper right to close the info window 8 84 Archiving Images Work in the database window Background Information Finding data Background Information Database queries Query by Example Query by Free Filter Query by SQL Query Save search filter Representation of the query results Your image analysis program offers three methods of finding images in a database You can use this query for a simple search for the entry of a field You can also link several fields using the AND link For a query by example you can use the wild card Searchtargetsare Field Entry all records beginning with letters Gold all record
79. you select all the sheet elements by drawing a frame around the whole sheet keeping the left mouse button depressed 8 Click the Group button in the Order and Group button bar to have the separate W sheet cells reassembled into a single object 9 Position the sheet keeping the left mouse button depressed and if necessary x adjust sheet size Adjust sheet size by moving one of the sheet edges with the mouse keeping the left mouse button depressed 10 You now change the size of the sheet To do this you keep the Ctrl key de shy pressed so that the sheet remains in the same position gt When adjusting the size of a sheet the font and font size remain un changed The separate values will thus be pushed closer together and in extreme cases overlapping 11 Click the Properties button in the Report Objects button bar to have the sheet formatted At the same time you alter the properties for all sheet cells Report Generator Inserting sheets Step by step You can automatically fill an entire report with Measurement Form Al2 680 database information Phase Analysis General Data Specimen Data Measurement Data comuhacted ty Mi Sperimer ELDig4si cordacted ori 09 Material tested by Dai Preparation Ares PhaseAn alysis Phase 1 0 42 Phase 2 43 106 Phase 3 107 244 Phase 4 242 255 O m a m m e m fe 1195 42 16 30 4734 80 23 61 4119 09 56 15 289 16 4071 42 14 64 4803 80 24 59 2864 44 52 568
80. 610616 Cancel Bese a Colorview Ilu PY Bw 22610616 Help Use calibration of active channel Info v Calibration Magnification Macro Input Display Format Exposure 50000 B TE Beit 2576 1932 M Activate esolution Sharpen jo B Online Shading corection Activate Illumination method Transmitted Light Mirror Horizontal I Vertical Camera Colorviews lu Pot MASA a filter Info Cancel Help e having an overexposure warning appear e enhanced contrast onscreen display of images even if acquisition conditions are poor via automatic or fixed scale contrast enhancement Automatic gain display or Fixed scaling e checking on current intensity distribution intensity mean of all 3 color chan nels during image acquisition using the online histogram e activating live overlay e setting the scaling of an image within its viewport Live overlay S Automatic gain display S Acquiring images Optimizing display Background information Configure Input x Info sv Calibration Magnification Macro Input Display Format Over exposure Display warming W Ondine histogram Overflow 0 50 Eje I Fealtime kT M Live overlay Automatic gain display W Activate Lett overflow 0 00 Be Right overflow 0 01 Fined scaling amp etvate Brimi DE Fight imi A098 B Image scaling Adjust to viewport H
81. A higher frame rate is attained due to the smaller amount of data being transferred The live overlay must be enabled for the partial readout The live overlay can be en abled via the Display tab located in the Configure Input dialog box Use the button with the red frame to define the area of the image which is to be read out SE 36 Acquiring images Acquiring images Step by step Step by step Determine image buffers and viewport for the image acquisition 1 Click on the image buffer within the image manager you wish to have the cam era image placed in gt The active image buffer will be color highlighted gt The viewport currently linked to the active image buffer will have a color header both in the image document and in the viewport manager 2 You wish to display the camera image in another viewport Simply drag amp drop the image buffer of the camera image onto the new viewport within the view port manager Then leftclick on this viewport Set magnification correctly before acquisition 3 Select the Image gt Set Magnification command to set magnification so that your resulting image is correctly calibrated e This is only necessary if magnification is not automatically read out via the microscope s remote control gt The Magnification list includes all those magnifications that you saved in the magnification table Image gt Configure Input gt XY Calibration gt Save 4 Click on the magnif
82. B images Background Information 3 Click on the preview window in the Define DCE dialog box so you can see how parameter adjustments affect the image 4 Adjust the Bandwidth and Enhancement parameters alternately The less band width the smaller the local differences in brightness which are enhanced The greater the enhancement the more these differences in brightness are accen tuated Keep adjusting until you find the optimal settings 5 Select the Quality check box to suppress artifacts located in areas of the same brightness caused by the DCE filter 6 Click the Execute button Use the DCE filter to in crease image sharp ness Easily over looked image detail thus becomes readily visible Filtering RGB images Background Information RGB Studio The RGB Studio consists of a group of commands especially developed for editing RGB images RGB Studio commands are located in the Oper menu You use the RGB Studio to filter color images e g using the following filters Gamma Hue Saturation In tensity Contrast Sharpen Average Remove Noise Oilify Posterize Mosaic and many others convert color images into 8 bit images using different color palettes edit color palettes rotate or clip color images superimpose color images or add a watermark break down color images into their color components using various color mod els colorize color images using one color assemble gray value images as
83. Before starting the backup carefully check the data in the File Storage dialog box L6 92 Archiving Images Archive data Step by step ep ge erie backup you will get McAi E important information about the backup Select Finish to let the storage assistant start the storage process with the Following settings process Please note that you Storage method Backup require at least two data Database C archivelbestmaizoo4itestmaiz004 apl mediums if you want to Destination drive E CEIDW save all of the database Volume size 703 MB files Temporary directory F TmpStorageDir Storage extent Complete backup Number of volumes needed 2 Back Cancel Help 14 Click the Finish button to begin the backup gt Your image analysis program copies all of the records for the first CD or DVD first to the backup directory and then starts the burning software gt Your image analysis program checks to see if the files were properly burned The test can take some time based on the drive because it is checked bit by bit After the test has successfully been completed you will be asked to remove the CD and to label it with the provided identifier gt After the test has successfully been completed your image analysis program deletes the files from the temporary backup directory to create space for the next CD s files gt 15 Label the CD accordingly 16 Insert the next empty data medium and follow the database
84. Calibrate Image command before having the scale bar shown WARNING The automatic scale bar is not a part of the image overlay It is a viewport property The scale bar is linked to the coordinate system of the viewport and is shown in a fixed position i e size position and font size remain unchanged even when you move the image within the viewport or change its zoom factor The calibra tion length will always be adjusted to fit the current zoom factor of the image in the viewport You may also have the unit automatically adjusted in order to avoid exces sively large or small numeric values SV 46 Acquiring images Showing scale bars Step by step Step by step Show scale bars 1 Load a correctly calibrated image into the active image buffer 2 Press Shift F4 to make the scale bar appear disappear onscreen You may also select the Image gt Scale Bar gt Show in Viewport command gt Scale bars appear in the lower right corner of viewports e Showing scale bars is a global setting This means that either you have scale bars shown in all viewports or in none at all The image document is divided up into four viewports in the above F 20x m Ee example All four view mki E n Q Q R eal ports show the same im qe ere a oe a ah So e a a paraan s j re bee ee ae age but at different 220 oe ress U zoom factors viewport image document Images 4 16 Bit Image 20 Oy x Ea r
85. Click on Start to begin animation of the model Wait until the anima tion has ended or interrupt it with Esc e The rotational direction and degree for animation is set in the ncre ment X Y and Z fields 3 Go to the Options tab Set the Width and Height of the output image Close the Rendering Settings dialog box 4 Activate any empty image buffer to copy the 3 D view area as currently shown into an image buffer Rightclick on the 3 D view area and then se lect the Copy to Image Buffer command A Editing models Background information Modifying 3 D surfaces Height Resolution Click the Modify 3D Surface button You will find the button in the lower left cor ner of the 3D window by default Some options contained in this dialog box are described in the following You can set the relative height of the model surface as you like Height is cor rectly scaled for calibrated height maps Models created using non calibrated height maps will have height values determined in proportion to image intensity The level of detail and how smooth the model surface is depend on how many height map pixels are used to compute the model This is what step width de fines Restricting image area for model Step by step a When working with a cali brated height image you can determine the height of the model surface via the data visualized length width and height above left If the height image is uncalibrated you
86. Creating 3 D surfaces Coloring models Step by step This pyramid shaped inden tation left was the result of a Vickers material hardness test The surface is shown including the texture image left and in single color dis play right e Select Single color to have the 3 D model displayed in a single color To select the color desired click the Colors button Doubleclick on the Front field and select your color Select the color of the underside of the model via the Back field e Select Texture to have the model colored using a texture image If you haven t yet loaded a texture image click OK to close the dialog box and drag amp drop the texture image onto the 3D window e Select Height coded to have the model texturized in proportion to its height over the bottom grid This means that a height of 0 is assigned a gray value of 0 maximum height is assigned the gray value of 255 All this to say that model valleys appear dark and peaks bright e Select Texture from height to have the model colored using the image intensities of the height image 3 Close the Modify 3D Surface dialog box Coloring models via palette 1 Click the Modify 3D Surface button Surface button bar along the upper edge of 3D window 2 The LUT list is where you determine whether you wish to have the model additionally colored via a lookup table or not No lookup table is the default 3 Select Height lines to have height lines shown on th
87. Field name cient sS Data fret ti sY I Input required EYDo cument Modification Tin M Organizational Field Document Replacement D Document Replacement T Cancel a Help New organizational field is set up Define Fields T Indexed for searching ae 24 x Field properties jeld list Name Client Project No Help Datatype Text Date J7 Input required Edit di Fixed Picklist Gi Time 7 Edit Don t expand PICHIst Gf Input N amp paAudio File Expand piciist on input P ByBits per Pixe Calibration Unit Channel Document Creation Date Document Creation Time Restrict input to picWlist entries 7e Document Fi Document I rerrerret Default Document Inse oo ument Modific ay Document Modificati r PA Reola value of last input iC Field Client OK TES Pan The input field for the client Quality Assurance Cancel to be filled out for each new roject Add proj Quality Assurance Change Delete Down A picklist determines which clients can be specified when setting up a project ddad Clear Sort Help i Sort P Automatic Ascending Descending Archiving Images Define database fields Background Information Define database fields Background Information Open the database You can open the database using the
88. ING RGB Images seirene a O 108 Interactive Image Measurement cceeccceeseeeeseeeeeeeeeeeeeeeseenesenseeoeeenes 111 Save load and edit measurement results oo ee eee cece eeeeeeeeeeeeeeeeeeueueneeueeaeenes 113 Create measurement sheets cccccseescceceseeeccceeeceeceeeececeeeeeeceeaeeeesseeeeessaeseneas 116 WSING StAtISHCS UNCUONS virseksa a jenaeacentactecekse E RA 119 Measuring arbitrary structures ccccccccesececeeeecceeseeceeseeceeueecseuseessaeeeseeseesseeeess 120 Optimizing work environment for measuring cccseecceceeeeeeeeeeeseeeeeseneeeseueeesaeeeens 124 Creating 3 D surfaces ssssnnssnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnmnnn nnmnnn 128 Creating models ccccccseesecccceeesceeceeeeecseeseeecseueeecseaeeeeeseeaeeessaaeseseesaaeeessseeeeenas 128 Editing Models nien E a E E 130 Colonna Models ernennen a E iene ad doit cnmaesi ses 133 Measuring Models renies e E EN 136 image ANALY SIS ccionn aaa aa aaa 139 Phase ANN AY SIS serora eet a N a 139 pelecting Particles cstcceccuastondsnnpuansvedunamocnuiesdobsucsavwten tanteutalecnasusd ee cmentavectaiataimauneads 141 image Dreparallon anni aeaile ne Wierd nad aar aia el 142 SENNOM ESHO S eai a th aneccrbet acc a aE 145 Deining detecthomarea zsoci ee e a E AE E 147 Deining detecto ersen E a 150 Meas rng DAMICICS ena Ea a a e a a 153 Editing detection INtCractively cccccsccecesseeceeseeceeeeeeceeeeeceeseesseseessaeeee
89. Image button in the Report Objects button bar to define a new image i object within the template page 4 Now you define a rectangular segment for the image object Define its exact size and position via mouse or in the Position and Size tab 5 Drag a representative image from the image manager or from an image data base and drop it on one of the image objects to better be able to assess how the images will look in later reports 6 Select the image object and click the Properties button in the Report Objects button bar to determine the properties of the image object 7 Check the settings in the Select and Move tab e Clear the Background object check box to define the image object as an image placeholder Objects that you define as background objects cannot be edited later on in the report e Select the Fixed Position check box to establish a fixed size and position of an image object for all reports These cannot be altered later on in a re port 8 Click the Clear Object button in the Report Objects button bar to remove the test image from the report object gt The lettering of the scale of length and the values of the automatic zoom will be replaced by number symbols 9 Copy the image object by pressing the Ctrl key each time you move the new image object to its intended position 10 Click the Save Page Template button and enter a new name e g ImageGal lery into the field 11 Confirm via OK to have the
90. NXN dialog box will be opened 5 Click the Window button gt The mouse pointer will appear within the image along with a red frame The preview window is defined via mouse while pressing the left mouse but ton Rightclick to confirm e All parameter adjustments made will appear immediately within the pre view area 6 Enter the number of times averaging is to be executed into the terations field The higher the iterations the greater the averaging Start out with 1 7 Enter the size of the neighboring pixel area to be used for averaging into the Size field e g 3 corresponds to an area 3x3 pixels in size e The higher the value the more the image is smoothed Artifacts will also be smoothed not just the actual edges 8 Continue to adjust both parameters until you have obtained optimal results Then you click the Execute button Increasing image sharpness 1 To increase image contrast select the Oper gt Filter gt Sharpen command e After suppressing noise or artifacts via a mean filter you can have the smoothed edges displayed sharply once again Accentuating image detail 1 Load the image and set the destination image buffer 2 Select the Oper gt Define Filter gt DCE Filter command e The DCE filter enhances small local differences in brightness Image de tails are thus accentuated the more general structural elements retreat into the background ZOL 108 Processing images Filtering RG
91. OLYMPUS User Manual analySI S Imaging Solutions for Light Microscopy Any copyrights relating to this manual shall belong to Olympus Soft Imaging Solutions GmbH We at Olympus Soft Imaging Solutions GmbH have tried to make the information contained in this manual as accurate and reliable as possible Nevertheless Olympus Soft Imaging Solutions GmbH disclaims any warranty of any kind whether expressed or implied as to any matter whatsoever relating to this manual including without limitation the merchantability or fitness for any particular purpose Olympus Soft Imaging solutions GmbH will from time to time revise the software described in this manual and reserves the right to make such changes without obligation to notify the purchaser In no event shall Olympus Soft Imaging Solutions GmbH be liable for any indirect special incidental or consequential damages arising out of purchase or use of this manual or the information contained herein No part of this document may be reproduced or transmitted in any form or by any means electronic or mechanical for any purpose without the prior written permission of Olympus Soft Imaging Solutions GmbH Windows Word Excel and Access are trademarks of Microsoft Corporation which can be registered in various countries Adobe and Acrobat are trademarks of Adobe Systems Incorporated which can be registered in various countries Olympus Soft Imaging Solutions GmbH All rights reserved Printed i
92. SR SS l lt image Comment templates for field ob SSS SN jects can be defined in a report template ae lt 4 Measuring Results Sheet Cell lt Sheet CellJ gt Type Function Remas image object placeholder for database All image properties described above apply to images image objects as well i e you insert images at varying magnifications either as links or copies into a record object text standard text to be printed Texts are usually used in record objects to sup along with every image plement the standard AutoTexts e g the se quential number is supplemented with the word image graphic lines object AutoText sequential image numera This type of AutoText is only available within a tion record object field objects automatic printing of sin Field objects are composite objects that are gen gle line contents of data erally at least comprised of the name of the base fields field and the field s entry automatic printing of Memo database fields multi line sheet cell placeholder for a special Many special Add Ins deliver standardized mea value from a sheet cell surement sheets which are always constructed the same way Insert the sheet below an image in the database Use this field function to acquire individual measurement results i e the G value of a grain size analysis into the record object placeholder for a sheet a Sheets diagrams or graphs which a
93. Special gt Preferences Acquiring images Calibrating inputs Background information e You may of course acquire a snapshot without having to go into the live mode first Calibrating inputs Background information Calibrating inputs Calibrating a logical input is for defining the calibration for all images acquired via this input The pixel calibration data is decisive in doing so The pixel calibration data in dicate which area of the object is covered by one camera pixel They are different for each magnification To acquire correctly calibrated images the input must be cor rectly calibrated Precalibrated When working with a light microscope the input channel can be precalibrated This inputs only holds true for cameras manufactured by Olympus Soft Imaging Solutions The pixel calibration data is calculated from the camera s pixel size and the microscope s total magnification During installation of the image analysis program you determine whether or not you can or want to use precalibrated inputs You will be informed via this dialog box during in stallation if a precalibra ce tion of the input chan for the Olympus Soft Imaging Solutions Colorview Il u camer nels is possible Select y the Use automatic calibration for the camera command to in stall precalibrated input M Use automatic calibration for the Colorview I u camera channels TY adapter magnification 1 00 Magnifications of the microscope objectiv
94. To adapt record objects to your database 187 To change the print size of an image 180 To create a new report template 200 To insert a sheet 193 To insert images from image database 186 To insert images from the image manager 179 To insert text objects 191 To use sheet cells in a record object 196 To use sheets in a record object 196 Report Templates 197 Object Templates 202 Page Template 199 To create new filed object templates 203 To plan report templates 204 To save report templates 201 RGB 103 RGB Studio 109 Rich Text Format 172 ROI 147 To set a ROI 149 RTF 172 S Saturation Filter RGB Studio 109 Save Images 41 48 To save images 49 scale bar 46 Index Adjusting to printer frame 46 Altering scale bar properties 46 Properties 46 Show 45 Showing the scale bar 46 Select device 27 Select Viewport Manager Pane 19 Selecting Measurements 122 Send email 53 Separating particles 142 To separate particles 143 Sequence image acquisition 41 Serial number 10 Setting magnification 36 38 Setting thresholds 145 Auto Parameter 140 To set the threshold value 145 Settings Measure 125 Shading Correction 142 To correct the background 142 Sharpen filter Camera Control 34 Sharpen Filter RGB Studio 109 Sharpness monitor 35 Software Protection 5 Solarize Filter RGB Studio 109 SRC files 170 SRD files 170 Statistic display interactive measuring 119 Status bar 14 Stretch Intensity Filter RGB Studio 109 System
95. You do not have to make an entry in the exposure time field when configuring the input e Exposure time may be interactively adjusted while viewing a live image To do this use the Camera Control dialog box Image gt Camera Control command during live image acquisition e The Sharpen filter may be activated deactivated in this tab as well via the respective check boxes Or use the Camera Control dialog box to do the same thing conveniently during live image acquisition If you are using intX the settings for the sharpen filter are adopted from the active input e The Camera field shows a description of your camera type Click the Info button for more information on the camera for example the current tem perature of the CCD chip and of the camera housing 6 Select a predefined camera resolution from the Resolution list The selected resolution influences the spatial resolution of the acquired images ct e Please note the larger the spatial resolution the slower the camera works in live mode and the longer the exposure times you ll need will be There fore it can make sense to define two channels with different resolutions You still use the channel with the smaller resolution mainly for the live mode whereas the channel with the larger resolution will be used for the snapshot image acquisition 7 Select the Online Shading Correction gt Activate check box to utilize the online shading correction Select the procedure u
96. a Ekke Messeren gg pye Length 148 Pixel E i ageU5 F Origin bik 0 wm 0 pm Measurements This is how you identify a measurement on the image If you have measured a very large amount of values you will find it especially easy to find them on the image rather than in the measurement display 1 Click the Image Link button located in the measurement display gt The pointer moves to the image window 2 Click on any measurement object in the image overlay gt The respective measurement value is shown in the measurement display SLL 116 Interactive Image Measurement Create measurement sheets Background information 3 Depress the middle mouse button or the Esc key to exit the image window Create measurement sheets Background information Measuring on numerous images Even if the measure ment display covers the image buffer list you maintain access to all the tabs of the image manager during mea surement Create mea surement sheet Data in the measurement sheet Editing sheets Before each measurement the images can either be newly acquired with your cam era or you can load already saved images in successive image buffers In both cas es please make sure that the image buffers list is always covered by the measure ment display in the measurement environment You can change the views at all times and again show the image buffer list To do this click on the List or Gallery
97. a page layout begin by inserting the elements that are to appear in the background e g a frame Every object you sub sequently insert will thus automatically be in the foreground Altering page tem Any and all alterations you make to a page layout have to be re conducted on each plates individual page of a report template Make use of the Select Page Template button in the Report Template button bar to edit individual template pages Determining the first Open the report template and click the Select Page Template button Then select one page of areport of the page templates listed for use as a cover page or first page of your report Now save your report and close the report window once the cover page has been activat 661 200 Report Generator Report templates Step by step Inserting new page templates Deleting page tem plates Editing page tem plates within a report Step by step Warning l ed When you then create a new report based on this report template the first page of the report to be opened will be this one There are two ways to insert new page templates within a report template e Click the New Page Template button to insert a blank page template into the re port template A blank page template will be automatically created and given a standard name page template consecutive number Click the Save Page Template button to alter the standard name e Base your new page template on an existing one
98. abace lage Oper Measure Anak Goaph CModde 5 do Window O0 S Be FOOLER RE Ri eRe Ke a7h gt ERK F Images 7 000476 9 65 X Bare Jaa Ano Frame displayed Upper in the overla O left al ent comer Information about eo fey the set frame idth 649 Pixel in the status bar thie Eas Fview View Pw 65 t 921599 a 649 304 Position of the idth x Height upper left corner Defining ROIs 1 Select the Analysis gt Define ROIs command 2 To delete previously set ROIs click the Delete All button ol gt 3 Enter a name for the ROI into the Label field e g Nucleus gt Any new ROI name will automatically be added to the Label list e Use the names of this list later on for other similar ROIs e g other cell nuclei You do this by selecting the desired name from the Label list before you define a new ROI 4 Select the method by which you wish to define the ROI in the Tools group Er Click the Freehand polygon button to draw the image segment of interest freehand gt The pointer will appear within the image While pressing the left mouse button draw the ROI e g the interior of a cell nucleus 5 Rightclick to return to the dialog box gt The polygon figure defining the ROI will automatically be closed gt The new ROI will be numbered and added to the Active ROIs list gt Another color is automatically matched with each new ROI The color makes it easier to identify th
99. age selection by clicking OK Archiving Images Insert Images Step by step 7 The Insert Image dialog box will open for each image which is to be inserted gt The name of the image buffer is given as a suggestion in the Record Name field unless you have defined another in the Database gt Adminis tration gt Database Seitings dialog box e g automatic record names gt The insertion mask contains all user defined database fields which you have selected using the Arrange Fields command for the Insert view and the Image data type 8 Fill out the database fields and click the Insert button to open the insertion mask for the next image gt The inserted images are now displayed in the gallery view of the database window 9 Click on the plus character in front of the selected database folder in the tree structure gt Inthe tree structure the images will be arranged as an image folder under neath the selected order You can now insert new images or other docu ments one organizational level below the images 10 Click on an image folder in the tree structure gt The preview window on the upper left now contains the thumbnail of the image folder The information regarding the image which you have selected using the Arrange Fields command for the Form View and the image data type is displayed on the lower right LZ 72 Archiving Images Insert data Step by step When inserting numerous images simultaneously in
100. ains unaffected If you save an image along with its overlay in the TIF format image and overlay will remain separate Graphic data can be saved managed using various methods a bitmap consists of single pixels a vector graphic of mathematically describable curves A line is de scribed via its initial and terminal points bitmap pixel graphic vector graphic Overlay objects may be arranged in different layers Think of these layers as if they were several transparencies which are placed over the image Each transparency i e overlay layer may contain objects The annotation layer contains all objects inserted using the overlay button bar func tions The data layer contains all information that your image analysis program automati cally writes into the image overlay for interactive measurements automatic particle detection or for histogram calculation The standard setting has this overlay layer locked i e you cannot select move or delete an object from the data layer You can label images in an overlay without over writing image informa tion because the overlay is simply placed over the image like a trans parency Your image analysis program uses multiple overlay layers for different kinds of in formation The data lay er is reserved for auto matic overlays which are generated by mea surement operations Use the annotation layer to label your images Overlay but ton bar Processing images Edit
101. am into a report Diagrams can only be internal graphics Some commands e g Histogram au tomatically generate diagrams Otherwise you use the Edit gt Diagram gt New com mand for a graphical display of values from a measurement sheet Diagram properties e Diagrams like sheets can also be used as placeholders e When enlarging diagrams the font size is correspondingly enlarged as well This is not the case with text objects or sheets Keep the Shift key depressed while adjusting diagram size This ensures that the length width ratio of the page re mains the same and the lettering will not be distorted e Diagrams cannot be rotated The buttons in the Rotate button bar are not avail able e To alter the background color of the diagram go to the Fill tab Text labels have nothing to do with this and remain black lettering on white e Determine the color and the width of the frame outline in the Line tab The line width of the axes is preset and cannot be altered Metafile format WMF stands for Windows Metafile Format a format used for data exchange be tween Windows applications Diagrams are inserted as Windows Metafiles After the RTF Export has been com pleted you can edit them in MS Word You can also e g alter font and font size within diagrams in Word Please note that font and font size may be altered simply by your opening the metafile in the graphic editing mode of Word Report templates Creating sav
102. an add new mea surement values to an already existing mea surement or delete sin gle or entire measure ments Save measurement results Warning Editing measurements Measurement results and image overlay Step by step Hi values The measurement display has its own button bar Use the buttons for example to de lete measurement values or to alter the presettings for the interactive measurement A Delete Measurement Image Link Show hide Statistics x e aeae Select Measurements Define Statistics Measurement Properties Image Manager x e S elles Alpe 1 Image lire 2 Image ma 3 Images i Fe Origin _ 0 0 bai Length 523 mm bose Length 600 mm a Length 577 mm ner Length 5953 mm All measurement files are linked to the image This link remains if you save the image in TIFF format Either use the File gt Save As command or insert the image into a database If an interactive measurement is linked to the image the measurement re sults are automatically listed in the measurement display when the image is reload ed The measurement files are only then saved with the image if you use the TIFF image format The measurement results are lost if you save the image in another format e g BMP or JPG A one time measured object can no longer be edited You can however delete ob jects with faulty measurements and remeasure them To do so select the name of an image in the tree
103. an switch on an artificial light source Light source position brightness color and degree of shadowing are de termined by you e LUT You can select any palette you like for the model The palette results in the model being colored according to height Or you can also have height lines shown in the model The resulting color of any point in the model is composed of all three above settings Saving opening 3 D A 3 D surface consists of a series of files The main file is the layout file which models has the W3D file name extension Any model alterations will automatically be saved in these files Each new model Oper gt 3D Surface gt Create is initially given the following standard name Surface3D w3a All model files are saved in the program di rectory at 3D Objects Surface3D If you wish to keep the model and not have it overwritten then select the File gt Save as command and save the W3D file using a different name in a separate directory All the other files of the model will automatically be copied to this directory After these steps your con tinued work will be with this copy of the 3 D surface TO open an existing model select the File gt Open command 3D Workspace w3d file type Step by step Texturize your model 1 Click the Modify 3D Surface button Surface button bar along the upper edge of 3D window 2 Select how you want the model colored in the Encoding list cel 134
104. any of this image information via the context sensitive menu Camera control gives you quick and easy access to the most important camera set tings and interactively during live acquisition too Camera sali Ea Exposure time determines for what length of time the camera s CCD chip is to be illuminated alters the value in pseudologarithmic steps Auto sets the value after the automatic evaluation of the current histogram during a live image Please note The image area is the basis of the calculation which you also deter mine for the automatic gain display When acquiring images with extreme contrasts you should not use the automatic exposure time Fluorescence images for exam ple are very quickly overexposed when you use it aa Color settings opens a dialog box containing slide controls which enable you to correct color errors and with which you can set the gamma values and the color saturation hite balance corrects a tinge either in the live image or in the snapshot Whi ta Use the button with the red frame to define the image area which is to be used to calculate the white balance Sharpen Filter activates deactivates the sharpness filter which makes the image sharper or on On Off softer depending on the sharpness filter settings Sharpen Filter Settings Use automatic gain display Histogram cal culation on en tire image cross hairs ROI Set ROI Use fixed scal ing
105. ard Use the Database gt Administration gt File Storage command to activate the data base wizard The wizard guides you step by step through the backup and the archiving procedures CD DVD Burner It is possible to access a CD or DVD burner directly from your image analysis program The Nero Burning ROM software is a prerequisite for this Please note the following points e Due to data security data will be written to the temporary backup directory when saving or archiving data Even when directly accessing CD or DVD burners you still require available storage capacity The required size of the available storage is equivalent to the capacity of the CD or DVD During file storage the system automatically checks if there is enough storage space on the drive for the temporary backup directory e The database files with the APL MTB and TNB file name extensions are always burned on a separate medium even if there would be enough space on the CD The reason for this is these database files must once again be modified after executing a successful burning procedure e Due to file security your image analysis program does not support the Multi session functionality from the burner software You cannot write anymore addi tional files to a CD or DVD after a successful burning Step by step Creating a backup copy of your database The backup is to be written directly to the CD DVD System You have access to a CD DVD burner You hav
106. atabase password Session password Warning You can limit the number of records that can be deleted in any one process in the Database gt Adminis tration gt Database Settings dialog box Step by step You can assign different passwords for every database The database password protects the entire database against unauthorized access The database cannot be opened by a user who does not know the password Remember however that a database password does not protect against access or manipulations through Windows Explorer Make a note of the password and store it If you forget the password you will no longer be able to access the password protected database Even the vendor of the database has no possibility of accessing the database without knowing the pass word A session password is not related to a single database but to a workstation Assign a password to prevent unintended and unauthorized manipulation of the structure of your databases All commands which affect the structure of the database are only available to the user who knows the session password for the software version The commands are deactivated for all other users The insertion and loading of data and all queries for a database with session password is also permitted for every user who can open the database The following commands are deactivated when the database is opened without the session password e Export record files e Database gt View gt Arra
107. ational field from the Available list into the Current list gt The customer will now be displayed in the insertion mask when an image is Inserted 11 Close the Arrange Fields dialog box by clicking OK LL 78 Archiving Images Work in the database window Step by step How to arrange database fields for the insertion mask Arrange Fields Available Curent EJEA Database fields can be arranged differently for different purposes e g insertions or queries View Type H E Form view Table View Print Et a Query by Example Insert N Arrange Fields Project is the database s organiza tional ID For an exper iment database however you could use the name Experiement rather than Project View Type Available Current m Info window Client Record Name agi Form wiew Y He Method i Horn Different database field can be important for different data types Jemove View Type Available Current tll m Info Window seas Project No Table View Observation Method Arrange Fields The organizational field are now also shown when inserting an image Record Name Client Preparation his a Quer by Example u Insert The insertion mask when inserting an image Insert Image E3 Record Name 1 REE Skip Client JUY 45 7 Cancel Project No Project 2 Observation Method ie Help
108. ator 19 124 Noisify Filter RGB Studio 109 O Oilify Filter RGB Studio 109 Online histogram 32 Online shading correction 27 Open Database 63 Organizational fields 60 Organizational ID 57 Origin of the Coordinate System Interactive measurement 125 Overlay Annotation layer 96 Burning 98 Data layer 96 P Partial Readout 35 Particle Filter 156 Particle parameters 153 To select measurement parameters 155 Particle Sheet Link 155 PDF documentation 9 Phase analysis 139 To execute a phase analysis 139 Posterize Filter RGB Studio 109 Precalibrated Inputs 37 Print Field codes for headers footers 51 image comment 44 Images 50 To define multiple image page layouts 52 Q Query results Database 84 R Record 57 Remote 38 Remove Noise Filter RGB Studio 109 Report Generator 168 Export Reports 172 File Format 170 New Reports 168 Report Templates 197 RTF Export 172 To export a report 172 To Generate a new report 171 To insert images from image database 186 To insert images from the image manager 179 To save a report 172 Report Objects 173 Adapt Record Objects 185 Align 176 Auto texts 189 Background Objects 199 Detail Zoom 180 Diagrams 197 Field Objects 183 Image Objects 177 Detail Zoom 180 Fit image into the frame 180 Move Image 180 Print magnification 178 Insert 176 Object Templates 202 Position 175 Record Objects 181 Resize 175 Select 174 Sheets 192 Text Objects 188 Text Variables 190
109. avail able within the template If you alter a report template these alterations only affect reports you create subse quently Existing reports based on the now altered template cannot be automatical ly updated You can also alter or redefine page and object templates within a report These tem plates are then however only available within that report and not for other reports that you create based on the unaltered report template Report template ilmagePage 2imagePage 4lmagePage plates Reports Report templates A report consists of multiple successive A report template consists of multiple pages pages All report pages can be but don t with different appearances and functions e have to be based on a single page layout g a cover page and a page for 1 2 or 4 The 1lmagePage page template defines images Besides these page layouts report what all report pages look like in the exam templates can also have object templates for ple shown record and field objects Document window s white gray backgroun Report template button bar The first field of the status bar indicates the The first field of the status bar is blank current page number total number of exis tent report pages The header of the report window shows the The header of the template window shows the name of the report If the report has not name of the report template along with the been saved yet it will have a standard name name o
110. base folder within the STAR database The name of the folder is defined by the central field of the database the organizational ID You define the organizational ID when creating the database and cannot change it for databases that already exist In an order database for example the order number is the orga nizational ID In a patient database the patient s name may be the organizational ID In an express database the Folder Name is the preset organizational ID Record A record is set up for every document that you enter into a database Images or other documents such as sheets texts diagrams graphs and reports for example can thus be stored in the database The records can be arranged hierarchically in the database LS 58 Archiving Images Define a database Step by step Database folder Database fields Database types Step by step The term database folder describes a folder within the tree structure of a STAR database The database folder is not a file folder at operating system level You will find a database folder only in the database window but not in MS Windows Explorer Database fields contain all the information that you want to store together with a document The entries in database fields are linked to the relevant document and allow you to easily find any document in the database Your image analysis program suggests three ways to create a database Express To store your documents use the predef
111. below the marked record A thumbnail preview is displayed for images diagrams and graphs The other document types are represented by icons Doubleclick on a record to load the record Doubleclick on a folder symbol to open the database folder Records which are linked to other data are represented in the gallery by a document icon and a plus character Click on the plus character to display the linked data in the gallery view Table If you have selected the table view the gallery in the upper right of the database View window is replaced by a sheet All the field information that you have selected using the Arrange Fields command for the Table View ts displayed To switch to the table view select the Database gt View gt Choose View command Button bar The button bar in the database window provides fast access to frequently used data base commands Status bar The status bar in the database window contains the names of the current record and the number of marked records Context menu The context menu contains frequently used commands You can open the menu by clicking in the database window with the right mouse button Tree XO structure Preview window Form View Gallery View G 6Z Archiving Images Work in the database window Background Information 4 The but ton Preview window Gallery shown E on the EE AEE EENET left change the data om CY E E base view The data base window is divided i
112. bjects 181 eZl 174 Report Generator Report objects Background information Background objects AutoText Selecting objects Selecting several ob jects Object Properties The buttons of the Re port Objects button bar are for all report objects which can be inserted This button bar is part of report generator and only appears when the report window is active You will find the button bar on the right edge of the user interface by de fault Image Objects 177 Inserting diagrams 197 Inserting sheets 192 Background objects 199 AutoTexts 189 or database information Diagrams sheets and single sheet cells can be defined as placeholders Use a placeholder s properties e g size and position to define the properties of im ages or texts you wish to later insert into a report Background objects are defined on the template page and appear on each page of the report which is based on this template page A company logo address or frame are common background objects AutoTexts are texts defined on the template page and which are updated for each new report page automatically Creation date and page number are typical Auto Texts You generally have to select objects first before you are able to edit them Leftclick once on the object to select it Selection markers indicate that an object has been se lected If you keep the Shift key depressed you can select several objects All objects you select will b
113. cal image operations Filters are not Filters include the gray values of neighboring pixels to compute a pixel s new gray value Contrast operations are so you can improve image quality in low contrast images Contrast can be increased within separate brightness ranges thus making structures visible which were unclear in the original image Image structures of similar bright ness can be accentuated or suppressed as desired What isa A histogram is an x y graph which shows the number of pixels versus the gray values histogram It shows you which gray values occur within an image and their distribution Peaks indicate gray values which occur frequently The histogram is another way the result of a contrast operation can be checked in addition to simply seeing what the image looks like Step by step Increasing contrast 1 Load an image with a weak image contrast into image buffer 1 2 Click the Image button bar gt Arrange Viewports button Select a 1x4 viewport EH arrangement Then you can compare the original image with images showing the results of various contrast operations Maximize the image window to full size 3 Set image buffer 2 to be your destination image buffer This is done by dragging and dropping the image buffer onto the Dest folder icon in the operands box 4 Select the Oper gt Intensity gt Maximize Contrast command gt The resulting image is written into the destination image buffer e This command tra
114. cannot therefore be removed from the list e The Available list contains available organizational fields The information in the organizational fields relate to all the records in a database folder 12 Select one of the organization fields in the Available list for example Client from the step by step instruction on page 60 and click the Add gt gt button gt If you now insert an image to a project the method of investigation can be entered in the insertion form The Customer field is provided by way of information 13 Use the arrow buttons to change the sequence of the database fields shown in the form view 14 Close the Arrange Fields dialog box by clicking OK Archiving Images Define database fields Step by step The insertion mask for p adding an image database fields that Ms lwne Available owe Alel belong to the Add 1 8 Info Window Record Name view and the image m e Form wiew Project o TE Method i AB Table View paration TE Bp Pririt 2 Query by Example Help data type ial Insert wef Project GJ mr Setta allah thie fie 2 rapt Get Default asss E Data Set Default Addo e P aa an ke fields e g Client will have been alread Fields 1 5 defined when e database folder was set Record Name Skip up and cannot be Order No Order 1 altered when data is eee Cancel F f servation method inserted into a database RR folder Preparation Help All req
115. ce Creating models 128 Illumination 133 Measure 136 Move 129 Open 133 Rendering 130 133 Save 133 Setting height 131 Setting resolution 131 A Acquiring snapshots 34 Adjusting colors 105 Analysis button bar 145 Annotation layer Overlay 96 Append Particles 160 Arrange Viewports 18 Automatic gain display 31 33 35 Average 106 Average Filter RGB Studio 109 B Backup copy Database 90 Backup Database 90 Black balance 35 Build number 10 C Calibration 37 Camera Control 29 34 Camera resolution 29 Classification of particles 161 Classifying particles 161 Color Separation 142 Color settings Camera Control 34 Configuration Software 22 Contrast enhancement 30 Contrast Filter RGB Studio 109 Create measurement sheets 116 Customer service 10 D Data layer Overlay 96 Database Export images 86 Insert Images 70 Loading document group 89 Open 63 Open database exclusively 63 Database fields 60 Data types 63 Default value 61 Picklist 61 Database folder 58 Database settings 57 Database window 79 DCE Filter 107 Default image name 41 Defining detection 150 Border particles 150 Excluding particles 150 Holes 151 Pixel connectivity 151 Delete Delete Measurement from Image 115 Measurement 115 Delete Particles 160 Detecting particles 141 Defining detection 150 Defining detection area 147 Defining Measurements 153 Detecting one result at a time 158 Displaying the particles in the overlay 162 Editing de
116. classes are to be calculated from the image see De fining a classification scheme 163 e Check to see if you are using the correct classification scheme Open the Analysis gt Classify dialog box The classification scheme utilized can be found in the Classification list Z9L Report Generator Report Generator Background information Report Generator What exactly does report generator do Automatic report generation Use report generator to have multi page reports produced practically automatically including images of a database or of the image manager Select a number of or lots of images from an image database and have them all added to a report using a sin gle command Full database integrated access Along with the images themselves that you get out of a database you can have all additional information on the images contained in database fields of image databas es automatically included in a report Sheets with important measurement results can also be automatically filled in Working with images A particular focus of report generator is being able to work with images in an optimal way norm enlargements are followed detail zooms can be inserted appropriate im age segments can be selected and more Texts Sheets Diagrams Graphs Most types of documents that you generate within your image analysis program can be inserted into a report Via report generator you can e g print out images along with relate
117. cluding the appended particles If you have deleted any particles their data will not be included in the sheet Classifying particles Background information Classification scheme Automatic Classification A classification scheme is comprised of a name a unit and a class division Particles are sorted via the classification scheme according to certain parame ters Particles can be sorted into 10 size classes for example You can deter mine the number of particles per size class for example You can also have the average gray values of all particles of a particular phase measured You define a new classification scheme in the Define Classification dialog box You have numerous possibilities in opening the dialog box e Use the Measure gt Define Classification command e Click the Define Classification button located in the Analysis button bar e Use the Analysis gt Classify command Click the Classification button e When you load or acquire a new image your image analysis program will use the classification scheme last used If you wish to use a different one then you may change it e Once you have conducted detection within an image your image analysis program will remember the classification scheme that was used on this image in the previous detection The next time you conduct detection with this image your image analysis program will use this same remembered classification scheme This is also true fo
118. considered upon insertion into the report When moving a sheet from a database to a sheet object only the sheet cells are inserted which were displayed during the insertion of the sheet If you ex plicitly want to determine exactly the sheet cells which are to be inserted into a sheet define a sheet object within the record object Formatting sheets a template cannot be defined for a sheet Each sheet you insert has to be formatted individually Sheet object structure your image analysis program converts measurement sheets before insertion into a report into a complex object made up of numer ous separate text objects Every single sheet cell is in fact a separate text ob ject You can completely disassemble a sheet into its component parts in a re port for editing purposes Editing sheets to be able to edit each sheet cell separately you have to break up the grouping ungroup Regroup each sheet after you have finished editing You can work with the sheet more easily when it is grouped A sheet that has been grouped together can be e g positioned as a single object Use sheets in record objects if you want to insert additional information from an im jects age database together with a sheet A sheet which has been defined in a record ob ject has an additional tab located in the sheet properties The Document Link tab en ables you to exactly define the sheet cells which are to be inserted into the report Report Genera
119. current directory in the Save in list Be lt P gt sure that you save your report template in the correct directory If the report template is saved in another directory it will not be offered in the New Report dialog box 7 Click the Save button to save the report template Save button to have the report template in its previous form overwritten by the 8 If you wish to save the report template after having made changes click the most current version Object templates Background information Object templates You can create your own templates for records and field objects These templates determine what your record or field objects look like and their make up Object tem plates are saved under a separate name within the active document You can then insert them into a report at any time You define object templates within a report tem plate generally so that you can use them with all the reports you create based on this template It is not permissible to import object templates from other report templates Edit object Mode The edit object mode is for selecting and editing the separate elements of a record object you have selected All other report page elements are not available for editing and are only shown onscreen for reference purposes The edit object mode is available within a report for editing individual record objects Field entries are not filled out in the edit mode when you drag an image from a data base into the imag
120. d e mails can lead to transmission difficulties It is thus not advis able to copy screenshots of an entire onscreen view into an e mail 4 With the gt About command open the About dialog box gt The About dialog box tells you what expansion version you have the build number and the serial number of your version as well as the operating sys tem being used e Please be sure and have all this information available when you contact our customer service analySI All Functions Copyright 1986 2007 5 0 Build 1217 Olympus Soft Imaging Solutions GmbH You can have the most important software data displayed by using the gt About command w OLTIpLUS s1s COM This program i registered to Benoit Varlet Olympus Soft Imaging Solutions Seral Number 528103 7 rBCr 390 Your key expires 01 07 2008 Microsoft Windows NT 5 1 Build 2600 Service Pack 2 Pentium processor A992 KB total memory Warning This program i protected by copyright law and international treaties Unauthorized reproduction or distribution of this program or any System Info portion OF it may result in severe civil and criminal penalties and will be prosecuted bo the mavimum extent under the law 5 Now all you need to do is to write us an e mail describing the problem you re having as precisely as possible incl snapshots if applicable Include the sys tem information as well Then send it to us at our customer s
121. d measurement sheets and diagrams on the same page Flexible Page Layouting Report generator provides you with the most flexible page layouting imaginable you set up your own template pages exactly the way you want them to be You generate your template pages only once These templates are the basis for your reports and ensure that the appearance of your documents is uniform MS Word compatible Via the RTF Export function you can have reports exported to MS Word 1 1 This enables you to communicate with fellow colleagues who may not have access to your image analysis program Creating reports Background information Reports and report templates Report window Exporting reports 172 Report templates 197 Ruler 175 Reports are used to document results in standardized form They usually consist of many pages which are similarly structured In order to make report creation easier a report is based on a report template The report template defines all page layouts and object templates that can be used in this kind of report You can never load and edit more than one report or report template at a time The report will be loaded into its own separate window Only one report page can be shown and edited in the report window at a time The report window has its own sep arate button bar and a status bar There are ruled borders and a grid for use as po sitioning aids Reports are opened within a separate win dow The functionality
122. d the desired field entries as well will be included in the re port Using sheet cells in a record object 1 Use the Record button in the Report Objects button bar to insert an existing record object 2 Click the Edit Object Template in the report window button bar to switch over to l the edit object mode 3 Click the Field button in the Report Objects button bar to add a new field object to the record 4 Inthe Select Field dialog box select the Sheet Cell entry and confirm with OK 5 Click the Properties button in the Report Objects button bar 6 Inthe Record Fields tab enter a description of the measurement value into the Fieldname field i e G Value 7 In the Sheet group enter the Filename into the field in order to insert the first attached sheet together with the record 8 Determine the desired sheet cell in the Sheet and Column field Should the in serted sheet not contain the specified sheet cell the field remains empty 9 Click OK to close the dialog box t 10 Click the Finish Object Editing button bar located in the report window 11 In the Finish Object Editing dialog box click the Exit without Save button EJ o Report Generator Inserting diagrams Background information 12 Pull a record with a sheet from the database onto the altered record object Inserting diagrams Background information Diagrams Click this button in the Report Objects button bar to insert a diagr
123. database Image compression You save individual images with the File gt Save As command You should save your images as TIF files Only when using TIF format are the additional image at tributes overlay image calibration channel data microscope data image comment saved together with the image You have the possibility of e saving images compressed e burning the overlay when saving e saving a 16 Bit image as 8 bit Images have to be in a specific format so that they can be read edited and saved The image format determines e g the image type image width and height file ex tension LUT position and pixel values Save Image as Tagged Image Format tif 4 4 indows Bitmap bmp j Aulabeltl JPEG JFIF jpg a Fubb_edy 515 MS DOS sis a Rubb_mal PC Paintbrush pcx Rubberti Truevision TARGA tga a Spheres PhotoShop 3 0 ped a Spheres2 Encapsulated PostScript eps Windows Metahle vamt SUN Raster ras WordPerfect wpa Macintosh Pict pct Save as type Portable Network Graphics png LEAD Kompression cmp Save ir File name Compression None If you have lots of images to save it s a very good idea to set up an image database The database eliminates having to manage image files and also provides you with a broad range of search options so that relocating the image s you need is no problem at all Your image analysis
124. deration e When you do define a background either the upper or lower gray val ue range is not taken into consideration 6 Select the Fixed option in the Histogram limits group Enter 0 into the Low er limit fleld 255 into Upper limit for 8 bit gray value images gt This setting means that the entire image histogram will be considered for calculating thresholds 7 Enter the number of existing gray value phases into the Phases field The example shown has 4 phases gt Suitable thresholds are automatically calculated via the histogram The color bar below the histogram shows the gray value ranges of each phase Warning 8 Select the Manual tab and click the Auto button to use the automatic thresholds If you do not execute this step the automatic threshold values will not be used 9 Confirm the thresholds you have set by clicking OK Phases can be automatical ly computed for gray value images Manual Auta Settings No of phases Background ee Set Rol fm def C Low High None 5 File Histogram limits Set Thresholds Ea C Dynamic seeeeeeneeee Lower lirit _ Upper lirit 255 B Urderflow oo a Overflow oo B z Cancel Help 10 Select the Measure gt Phase Analysis command gt Your image analysis program will create a measurement sheet show ing the absolute area and proportional area in of all the phases Phase analysis results ap pear in a measureme
125. e 4 Open the image database containing the fields you wish to make use of for fu ture standard reports 5 Use the Record button in the Report Objects button bar to insert an existing record object Z8l 188 Report Generator Report objects Background information Text objects gt The inserted record object has already been selected 6 Click the Edit Object Template in the report window button bar to switch over to the edit object mode gt The edit object mode is where you can select and edit the separate ele ments of the record objects selected Any other objects defined on the page are displayed with a crosshatching pattern only for reference pur poses 7 Select all field objects that you wish to replace with your own field objects select and Del Delete e g the Application and Image Comment 8 Click the Field button in the Report Objects button bar to add a new field object to the record gt The Select Field dialog box will be opened This is where you ll find all da tabase fields that are defined in the active image database 9 Select the check box in front of the desired database fields and confirm with OK gt The mouse pointer will change its shape Click on the spot approximately where you wish to have the field objects placed Once the field objects have been inserted you can position them more precisely gt The Select Object Template dialog box will be opened This is
126. e Nero Burning ROM software requirements 1 Check the settings for the temporary backup directory Use the Special gt Pref erences command Select the path to which the data is going to be temporarily stored to from the Temporary storage directory field located in the Database tab e Please note There must be sufficient space for burning in the directory to D which the temporary backup directory has been stored 2 Check the directory name under which the database files of the database are stored To do this select the upper most entry in the database s tree structure located in the database window The database path is shown in the form in the lower right 3 Place an empty CD or DVD in the burner 4 Use the Database gt Administration gt File Storage command to call up the file storage wizard You can directly access CD DVD burners directly from your image analysis software In this case the burner is going to be shown as an individual entry in the list of destination drives S Archiving Images Archive data Step by step 5 Select Backup Click the Next gt button 6 Select the database you want to backup To do this enter the path name of the database in the field or click the button to select the directory Click the Next gt button 7 Select the destination drive for the backup Your CD DVD drive is explicitly shown in the list e Please note Select the burner from the list
127. e Display tab 3 Select the Display warning check box in the Over exposure group 4 Enter 0 5 into the Overflow field gt The program will then caution you Warning Over exposure as soon as more than 0 5 of the image s pixels are white during an acquisition 5 Select the Activate check box in the Automatic gain display group gt Now the image will always be shown with enhanced contrast onscreen no matter what the actual illumination conditions are Please note that over exposure and or over illumination cannot be corrected by the automatic gain display 6 Enter the value 0 01 in the Right overflow field gt Now 0 01 of the brightest image pixels will be displayed white onscreen e Use the right overflow value to prevent pixels which are too bright from in terfering with the automatic gain display e A Left overflow value cannot be defined for the ColorView lu 7 Select the Online Histogram check box to check the actual intensity distribution during a live image acquisition and to appropriately adapt the exposure time Intensity mean value of the three color channels gt The histogram will appear during live image acquisition automatically gt In addition the minimum mean and maximum intensity values of the cur rent image will be shown The percentages refer to the camera s maximum possible value For a 12 bit camera this value is 4095 for an 8 bit camera 255 ce 34 Acquiring images Acquiring images
128. e E Finish Object Editing Edit Object Template Leave Page Template Save Page Template Edit Page Template New Page Template Save Report Document Redo Undo You can only display one page in the report window Use the first buttons of the Re port button bar to page back and forth through a report When paging the current re port page will automatically be saved If you want to get to a particular page fast enter the page number into this field and confirm via Enter Click the Add Page button to add a page to the active report at any place After click ing the button select where the new page should be inserted You can add a new page either in front of the active report page or at the end of the report You have to indicate a page template for each page This determines the pages ap pearance s The newly added page will become the active page no matter what page was being shown before the new page was inserted Click the Delete Page button to delete the report s page which is currently displayed in the report window You have to confirm the deletion of a page Any and all image files and thumbnails in connection with the page will also be deleted Images inserted into a report as links will of course not be deleted Define the page format for the current report in the Report Properties dialog box Bor der and Format groups In addition determine some of the properties of the Graph ical User Interface GUI
129. e Properties tab This is where properties specifically for image objects are made available You can alter the image properties that have been proposed within the report template for individual images within a report at any time e The Fit image into the frame option located in the Magnification group is set by default Your image analysis program then calculates the most ap propriate magnification based on the calibration data for the size of the im age object 4 Change the magnification option and select the Use fixed magnification option gt The edit field suggests a magnification for each image with which the im age can be completely displayed in the image object 5 Enter various constant magnifications into the field and confirm by clicking Ap ply gt The size of the image object is what determines the maximum print size of the image The lower left segment of the image is all that will be shown be cause the image is larger than the image object e To move an image around within the frame click the Move image button in the Report Objects button bar 6 Select the X check box located in the Scale group to include a scale bar under neath the image being printed Select one of three possible scale bar types from the list The length of the scale bar is calculated from the pixel calibration data of an image and automatically adapted for printing Warning D The automatic scale bars are only accurate for images that are correctl
130. e ROIs on the image 6 Repeat steps 3 5 to define any further ROls for this image 7 Click the Save button to save your defined ROls for later usage with sim ilar images 8 Exit the Define ROIs dialog box via the Close button 9 Use the Analysis gt Draw ROls gt Into Overlay command to have the de fined ROls displayed in the overlay 6f L 150 Image Analysis Detecting particles Background information The example shows two ROIs defined and displayed in the overlay During a par ticle analysis the program only searches for particles within the ROIs e Please note if you make any additional changes to the ROIs now the overlay will not be automatically altered accordingly male IRQ QA G Pi D n Defining detection Background information You set the parameters for detection in the Define De tection dialog box Most pa rameters are only set once since they usually do not change for the same prob lems Excluding particles Border particles Define Detection Detection Classification Flesuts Particle filter Minimum O Fisel F Fill holes IY Use ranges Border particles amp Truncate Include C Include 50 3 In range B J62 i Exclude Total count Search area Frame C Alls C Mask Fisel connectivity Adjacent borders 4 Include diagonals Measurements File Execute
131. e Single Image tab to define header and footer position e Define borders in cm in the Border group Have a look at the illustration right to see what the various fields are for e Both headers and footers may have multiple lines of text If the text is too long not all of it will appear when printed i e it will be clipped e Select the Fixed image ratio check box to maintain the image s original length width ratio when printed out 3 Select the first Header Footer tab the first one on the left going left to right to define headers and footers for the whole page e Enter the text desired into the Header and Footer fields e g page Page date Today to have the page number and current date print ed on the page 4 Select the second Header Footer tab to define a different caption for each im age e Enter e g Name into the Footer field so that the image s name will be printed below the image automatically e Select the Print scale bar check box to have a scale bar printed below each image e Select the Print page header footer check box to have the page headers and footers defined in step 3 also printed when you print out 5 Select the Multiple Images tab to define the images position on the page e Define how images are to be positioned when printed out in the Image tiles group Enter the number of images to be printed out across i e horizontally into the Horizontal field and the number of ima
132. e da tabase File name The file name is the name the image is saved as on the hard disk for example Record name The record name is the name the image is saved as in its database Default image name At image acquisition the image is named according to a default name This presetting can be altered Special gt Preferences gt Image acquisition gt Prefix for images In cremental number Image buffer for The image is written to the active image buffer by default during acquisition If an im image acquisitions age is already in the image buffer it will be overwritten during acquisition Therefore it is recommended to check the image buffer for any acquisitions before starting the image acquisition LY 42 Acquiring images Saving images Background information Macros for your input channel Warning amp To avoid accidentally overwriting images when acquiring images you have the fol lowing possibilities Use the Special gt Preferences command Select an appropri ate entry from the Image acquisition gt Sequence list located in the Images tab e None An acquired image is written to the active image buffer Should this image buffer already contain an image that image will be overwritten This entry is pre set by default e Image buffers All Your image analysis program will now automatically select the next image buffer before each new image is acquired Should this image buffer already contain an image t
133. e icon for a user defined organizational field 8 In the Define Fields dialog box click the Close button to complete the definition of database fields Click the button with a yellow star on it to set up Define Fields a new database field Je Field properties Field list h i Ob t Method In the Available Fields Project No a See cman list select a database Datatype Text field to view its Observation Method F Observation Metho j Edit properties in the Define Ea Date Input required ii Fields dialog box dey bits per Pixel dy Calibration Unit dychannel i Expand picklist on input 2 Document Creation Date d24Document Creation Time 2 Document Files Size d24Document Insertion Date Default 24 Document Insertion Time C Yalue of last input 424 Document Modification Date 2 Document Modification Time 2 ie i pont expand picdist on imput in Restrict input to picklist entries Arrange Fields 9 Use the Database gt View gt Arrange Fields command 10 Inthe View Type list doubleclick on the Insert entry to display all data types for the insertion mask 11 Mark the Image entry gt The Available and Current lists now show all user defined database fields e The Current list already includes the predefined Record name field and newly set up method of investigation field The Record Name field must be filled in for every record which is added to a folder in the database It
134. e indicated by selection markers the last one you select has gray mark ers and the rest white Or keep the left mouse button depressed move the mouse to draw up a frame that encompasses all the objects you wish to select You have numerous possibilities to alter the properties of an object e Doubleclick on the object e Select the object and then click the Properties button in the Report Objects but ton bar e Select the object then rightclick and choose the Properties context menu com mand Select Objects Move Image Properties save Properties As Default Line Polyline Polygon Rectangle Polycurve Closed Curve _ Ellipse Report Objects Graph Diagram sheet Field Record Clear Object Fit Frame to Image Detail Zoom Image AutoText Text Size and position Altering object size via A mouse Altering ob ject position R via mouse Positioning objects approximately Fine tuned posi tioning Use the buttons of the Position button bar to fine tune your positions Positioning aids Status bar Ruler Grid Align button bar The buttons of the but ton bar are only active if numerous objects have been selected Report Generator Report objects Background information You can alter the size and position of all report objects either in the object properties by entering absolute numeric values or alter them directly with the mouse You can use the ruled borders of the
135. e measurement values from var ious images to one sheet the unit for all the images from the image calibration of the active image buffer is adopted The possibilities of editing measurement sheets which have already been created is rather limited You can alter the headers of the individual columns and hide values with the auto filter You will find all commands which have to do with sheets in a sep arate context menu You can open the menu by clicking on a sheet with the right mouse button Step by step ma o The Create Measure ment Sheet dialog box lists all the images on which measurements have been made The active image is marked This is where you de cide if the measurement results of numerous im ages are to be exported to a common sheet or to separate sheets Interactive Image Measurement Create measurement sheets Step by step It is not possible to delete values or edit single values In this case you delete the measurement values either in the image or in the measurement display and create a new measurement sheet This is how you measure numerous images Distances are to be measured on numerous images and then later exported together to a sheet 1 Load the images to be measured 2 Click the Measurements Bar button located in the standard button bar to switch to the measurements environment 3 Maximize the size of the image window so that you have the largest amount of space possible for displaying the
136. e model Click the LUT button to adjust distance thickness and color of the height lines as well as the color of the surface 4 Select From file to select a LUT for the model You load the LUT file desired via the LUT button The Lut directory in your program installation contains a number of predefined files The LUT assigns a color to each height value gt The colors provided by the LUT selected are transparent This means that e g if the model is a solid color the model color will blend with the LUT colors 5 Clear the Modulate LUT check box to have the model colored using the colors of the LUT selected only This cancels the encoding 6 Close the Modify 3D Surface dialog box Creating 3 D surfaces Coloring models Step by step The coloring of the surface has now been height en coded left Additional height lines along with grid and calibration data are shown on the model You can select a LUT for the surface in this case called Thermal right Lighting up your model 1 Click the Modify 3D Surface button Surface button bar along the upper edge of 3D window 2 Select the Enable light check box to have your model illuminated using an artificial light source 3 Close the Modify 3D Surface dialog box 4 Click the Rendering Settings button S D button bar along the upper edge of 3D window Select the Light tab 5 Define the intensity of this light source in the Intensity
137. e object This ensures that the labelling of the fields remains gen eral when you insert a new record object Creating new object A rule of thumb for all templates you generate within report generator you can only templates generate a new template by editing an existing one To generate a new object tem plate for a record object you first insert a record object edit it and save the template under a different name Object templates are listed alphabetically Use this to your advantage and pick a name for object templates you frequently use that starts with a letter near the begin ning of the alphabet Deleting object tem You now edit an object template and then terminate the edit mode immediately Se plates lect the object template from the object template list in the Finish Object Editing di alog box and click the Delete Object Template button Once you have deleted all the templates on the list your image analysis program will offer you a standard template as soon as you have inserted a new record object Standard object If a report template does not contain any defined record objects your image analysis templates program will add a standard record when you click the Record button As soon as you have defined your own object template for record objects the standard record will no longer be available Therefore if you wish to be able to use the standard record later on then save it Report Generator Object templates Step by step
138. e pages that are defined in the current report template listed within the dialog box De pending on the report template you ll have very different page layouts available 8 Select the desired page template and confirm via OK gt You ll now see the newly added page within the report window The select ed report template page influences the appearance of the page gt The status bar shows the current page and the total number of pages the report has gt The buttons for paging backwards or forwards are now available LZ 172 Report Generator Saving Exporting report Background information Saving a report 1 Press F8 to open the Preferences dialog box and select the Report tab gt You ll find the standard path for saving reports and templates in the Direc tories group gt Your image analysis program will propose a standard directory for saving reports the Report directory is a subdirectory of the root directory 2 Enter the path name where you want to save your future reports into the Reports field e g C Reports ProjectXYZ e lf the report directory does not yet exist click the button next to the Re ports field Click the Create New Folder button in the Select Directory dia log box to set up the directory 3 Confirm the new report path via OK 4 Click the Save button in the Standard or Report button bars gt If you are saving the report for the first time the Save Report Document dialog box wi
139. e range Adjusting contrast arbitrarily 1 Load the image and set the destination image buffer Click the Image button bar gt Single View button to see all contrast adjustments at optimal size within Lea the original image 2 Select the Oper gt Intensity gt Modify Gray Values command gt The Modify Gray Values dialog box shows a histogram of the image red and a transfer function blue Linear transfer is the default The image re mains unchanged e Any contrast adjustments you make appear within the image immediately 3 Adjusting contrast and intensity e g slide the Contrast slide control to the right You will see how the image changes as its contrast is increased 4 Now load one of the transfer functions in the Function list e Square Root and Logarithm increase contrast in the dark image areas and lessen contrast in the bright ones Square and Exponential do the opposite 5 Defining your own transfer function draw the function by hand The curve is drawn by moving the mouse pointer across the x y diagram while pressing the left mouse button 6 Once you have optimized the image as desired click the Change button The dialog box shows the histogram of the original image The orig inal image only contains some of all possible gray values The exist ing gray values range from 100 230 The transfer function shown is Max Stretch This corresponds to what the Maximize Con trast command doe
140. eatedly until all documents have been filed 9 If necessary expand the database folder in the tree structure in which you have inserted the documents To do this doubleclick on the name of the database folder or click on the plus character in the tree structure nodes gt All inserted documents are listed under the record in the tree structure gt Each type of document is identified by its own icon gt The gallery view shows all records which are below the marked tree entry Your image analysis program creates a thumbnail preview for diagrams The other types of documents are represented by icons gt The record name is used to label the thumbnails in the gallery view To change the record name for documents select the Database gt Edit Record command Archiving Images Inserting documents Step by step Inserting documents amp Database01 apl _ oy x gt amp Additional documents are inserted below this Project 2 EN record Until now the folder contains the following per Field value ject 2 Project Ho Project 2 1 Image record DCE Fuad 2 Documents e Time 16 23 Date ef U2 2007 U5 Client Lei are inserted wf Diagram Diag 9 raphil j Sheet line grating Ki Cancel C l b All Insert Documents Current document Sheet inset N File name Sheet sts Skip M Prompt forfilen Tyre a ner x Selectior Curent document
141. eck box in the Send email workspaces via e dialog box to include a Workspace wos file along with the other documents you re e mail mailing The recipient can thus open the workspace along with all images and documents and display these in their original onscreen arrangement To do this the recipient will have to save all attachments in a separate directory To open a workspace along with all other documents select the File gt Workspace gt Open command The size of your e To receive a warning message when the size of your e mail attachments exceeds a mails certain limit which you may set yourself go to the following tab File gt Send email gt Preferences gt General The following are possibilities to reduce the size of your e mail e Leave out some documents e Compress images Go to the Image and Report tabs in the Send email Prefer ences dialog box to do this eS 54 Use the Image tab to set the file format for all im ages that you e mail The Save Image Op tions dialog box enables you to determine for the TIF format whether or not and how the images are to be compressed You define whether or not 16 bit images are automatically convert ed to 8 bits and whether image overlays are burnt into the image be fore being sent Please note that the options for saving images are not the same for all image formats Use the Report tab to determine the file format for the reports to be sent The RTF format
142. ectory Simply press Ctrl A The File gt Open command is context sensitive This means the Open Image dialog box only appears if an image window is active If a text document is active the Open Text dialog box will appear etc The Open button is in the Standard button bar To have a look at the dropdown list of all the various commands for opening click the arrow beside this button After you have loaded an image it will be displayed in the image manager Image type image name and resolution are directly displayed in the image manager The displayed information are somewhat different depending on whether or not you have set the list or gallery view in the image manager image Image Number Name Colordot By MER 318 x 223x 24 Image Resolution Possible image types are values shown in color Image Thumbnail Number Image Empty image buffer Image Name A gray value image can be comprised of 256 8 Bit or 2 8 16 Bit gray A binary image is comprised of 2 gray values black and white A false color image is an 8 bit gray value image whose gray values are A true color image or RGB image is comprised of 2 colors 24 bit A Fourier image is a 32 bit image made up of real and imaginary numbers of 16 bits respectively First Steps Loading images Step by step Step by step Dialog boxes for loading files are based on stan dard MS Windows dia log boxes The d
143. ed text You can replace the lt organizational ID gt with a text of your own preference e lt Date gt is a wildcard for insertion date The date format depends on the current settings of the operating system Your image analysis program uses the short date format selected from the local settings of MS Windows e lt Cons No gt is a whole number which is increased by 1 Every number is issued exactly once If you delete the last record with the consecutive number 10 then the next record will be given the number 11 Creating a new database folder You have created a project database with the organizational ID Project If you have defined a different organizational ID for your database for example Order No or Customer No then replace the term Project with your organizational ID using the following step by step guide 1 Select the Database gt Insert gt lt Organizational ID gt command The exact command is created dynamically and depends on the organizational ID of the active database If your organizational ID is called Project the command name is then Database gt Insert gt Project gt The insertion mask shows all database fields which you have defined in the Arrange Fields dialog box for the Insert view and the Project data type 2 Enter the required information in the Insert Project dialog box or select an entry from the picklist Fields which require an entry are marked by an exclamation mark Archivin
144. ed workspace analysis Simply click the third button in the Workspace button bar 5 Then load an image your database a sheet and a histogram All these docu ments will be positioned according to your workspace layout Creating workspaces to use day in and day out 1 Select the File gt Workspace gt Save as command In the dialog box enter the name of the workspace e g date Select the Load documents check box Se lect the Confirm save on close option Close the dialog box gt The fourth button now represents this workspace e Atthe end of your workday save all images you wish to retain Any images lt P gt that have not been saved will be deleted without any prior warning and are thus lost for good Close down your image analysis program Click Yes when a message ap pears asking you whether or not you wish to save this workspace All doc uments that have not been saved will result in similar messages Save those documents you wish to hang onto The next time you start up all those documents will be loaded automatically as well Acquiring images Acquiring images Background information Acquiring images Warning l Your image analysis program supports a wide array of cameras and acquisition de vices The commands for acquisition depend on the acquisition devices or cameras being used The functionality can therefore diverge considerably from what is de scribed here Divergences occur between a digital camera
145. efine RGB Adjust ment dialog box provides slide controls and a field for each of the three color compo nents red green blue Slide controls are for fast less precise adjustment of color values Once you have approximate values use the fields to fine tune the settings entries can be made manually directly into the field or click on the arrow keys DEFAULT SETTING when you open the dialog box the parameters of the most re cently conducted color adjustment appear as the default setting The table below shows what parameters can be adjusted The range of available val ues is defined by the lowest and greatest value The middle value means the image remains unchanged command parameter value range ity Adj Brightness 1000 0 1000 Contrast 1000 0 1000 ASi Intensity 1 1000 10 11000 E Hue 360 o 360 _ Saturation 1000 0 1000 RGB Adjustment Red 255 J0 1255 Green 255 0 255 Blue 255 0 255 contrast 1000 brightness 200 HSI Adjustment The parameter intensity hue and saturation have changed in the top part of the image left Intensity 200 in creases brightness center A mid value ca 200 results in a maxi mum change in color A maximum value of 360 results in the original im age Negative and posi tive values cause the same kind of color change right Saturation 1000 is maximum Step by step Processing images Adjusting image color Step by step saturation
146. ement commands for the 3D window are located at Measure gt 3D Measurements Various geometrical parameters of the model surface can be measured e absolute position of a point on the surface x y z distance between two points on the surface height distance z1 z2 polygonal length polygonal perimeter Shift polygon length area Activate the 3D window to conduct your measurement and then select the com mand desired You define all measurement points interactively on the surface of the model e The results are written into a measurement sheet e Point markers and connecting lines are shown in the view area to indicate measurements of distance height distance position and polygonal length e Points and lines are not a part of the 3 D model and thus not saved along with it but instead along with the sheet Points and lines can be hidden shown at any time 3D views including points and lines can be archived by copying a particular 3D view area into an image buffer and then saving that image e Cyclically varied colors are used for displaying distance height distance position or polygonal length measurements of a measurement series in the measurement sheet and the view area Points set erroneously can be deleted from the 3D window and from the sheet successively press Shift and then leftclick to do this In order to attain accurate measurement results the height map must be cali brated correctly X Y calibration and image in
147. en the results are exported 7 Check to see if only the particles with the desired area are detected If you still are not satisfied Add the excluded particles again by clicking on an even smaller particle now displayed as hatched Or you exclude even more particles from the detection by clicking on a larger particle 8 Rightclick to return to the Define Measurements dialog box gt The interactively found limits for the particle filters are displayed both in the Filter Range group as well as in the Selected Measurements list gt The Use ranges check box will be selected in the Define Detection di alog box e If the particle filter selected does not yield the results desired select another filter The result of the modified filter is immediately shown on the image 9 Now you can define particle filters for other measurement parameters with out having to exit the dialog box The separate filter criteria will be connect ed via a logical AND operation in order to further restrict the number of particles detected gt Please note All filtered particles completely disappear from the over lay as soon as you have selected another particle parameter 10 In the Filter Range group click the Reset Maximum Minimum button to deactivate the particle filter for the active measurement parameter 11 Click on OK to terminate definition of measurement parameters 12 Select the Analysis gt Particle Results command gt The measure
148. enhancement which evaluates the currently up dated histogram automatically recalculates the fixed limits for the current camera settings opens the dialog box in which you can redefine the fixed limits for the fixed scaling contrast enhancement corrects the image background The program calculates the mean value for each color channel in an area ROI which you defined These values are subtracted from all pixels in the entire image The black balance is to be used predominately for flu orescence acquisitions in order to balance the undesired background in the acquisi tion Please note Do not use the black balance with brightfield acquisitions If you did you would change the colors in the images Use the button with the red frame to define the image area which is to be used for the black balance shows hides the sharpness monitor The sharpness monitor consists of a dialog box in which a relative measurement of the sharpness is displayed by a changing bar which can vary between Blurred and Focused In doing so the green bar shows the maximum sharpness reached since the live acquisition was started The black line shows the minimum sharpness reached so far Use the button with the red frame to define the image area which is to be used for calculating the image sharpness enables quick live acquisitions A rectangular part of the image is defined for the partial readout to which the readout is limited during the live acquisition
149. er than 1 when dealing with very small particles which are only a few pixels in size In doing so we are dealing with a rounding error You can preset the software so that results which are greater than 1 are automatically set to 1 To do so use the Analysis gt Define Detection command In the Results tab select the Shape factor limited to 1 check box Image Analysis Measuring Particles Step by step ECD Distance The ECD value is the diameter of a circle which has the same area as Equivalent Cir the particle cle Diameter Phase Name Name of the gray value or color threshold range as defined in the Set Thresholds and Set Color Thresholds dialog box Hole Count The number of holes in a particle Phases for particle The particles detected are those within the gray value or color value ranges de detection fined All phases that you defined via the setting of thresholds will be consid ered This is why when setting thresholds you should delete any phases not needed for detection Particle Sheet Link The measurement sheet and the image of the detected particles will remain connected up until the next particle detection you conduct e To locate particles within the image according to specific particle results simply doubleclick on the line s number which has the results of interest to you e To determine the measurement results for a particular particle within the image select the Analysis gt Particle Sheet Link c
150. erences gt View gt Allow tiling and cascading of im age window check box Then select the Window gt Tile Vertical menu com mand 3 Select the File gt Workspace gt Save as command e Enter a name for your workspace into the File name field of the Save Work space dialog box e g analysis e Disable the Load documents not only layout check box so that only the layout of the GUI is saved and not any specific documents e Select the Do not save option to ensure this workspace remains un changed when you close it e Click the Save button fc 24 First Steps Saving GUI configuration Step by step Loading workspaces 1 Activate the Workspace button bar This is done by selecting the following check box Special gt Edit Button Bars gt Button bars gt Workspace gt This button bar has 5 buttons which represent 5 workspaces The first two buttons are already assigned to the predefined workspaces called nor mal and report The third button represents the new workspace you have just defined analysis e To make any changes as to what workspaces the buttons represent sim ply use the File gt Workspace gt Define Menu command 2 Let s have a look at how a workspace can be used First load a different work space e g the predefined workspace called normal Simply click on the but ton for this workspace the first one to load it 3 Close all documents 4 Now load your own user defin
151. erted image The Database gt Edit Record command enables you to provide data about all of the inserted images at a later time The record name in this case corresponds to the image names e Database Input Mask An acquired image is written to the active image buffer and simultaneously inserted into the active database The input mask is opened after each image acquisition enabling you to put all data with regards to the im age directly into the database during image acquisition You can for example reissue the record name for each image The input channel concept includes defining basic macro commands for the input channel Select the Macro tab in the Configure Input dialog box to enter macro com mands to be executed either before or after the acquisition of an image e You may e g set magnification before image acquisition To do so enter the following row into the Preprocessing steps field SetMagnification Please note the following when working with ColorView u Do not define this com mand in the input channel when you are using the online shading correction The on line shading correction works with reference images which depend on the selected magnification If you change the magnification after having started the live image a false reference image will be used for the correction e You can for example adopt the scale bar into the image overlay after image ac quisition To do so enter the following row into the Postp
152. ervice e mail ad dress The gt About gt Sys tem Info gt Send com mand opens the window with the automatically generated e mail form you use to contact our customer service All necessary system info is automatically includ ed in this e mail form All you need to do is enter a precise description of the question problem you re having and then just click on Send up per left button e mail window button bar to send it off to us Step by Step analySIS Any questions or problems Step by step support osis olympus sis com e The easiest and most convenient way to contact our customer service is by using the automatic e mail generation function The gt About gt System Info gt Send command will automatically gen erate an e mail form which you can then send to us when you ve added the relevant details of the problem you re experiencing Before sending it off to us please read the notes in the e mail window concerning the infor mation on your system which will be sent to us via this e mail Should you not be able to send an e mail from your PC use the gt About gt System Info gt Save Info command to save the files so that you can send the e mail from another PC e Please feel free to call us or fax us as well at the following numbers Tel 49 2 51 7 98 00 0 Fax 49 2 51 7 98 00 6060 Dear apalysis l user This functics has generated an email with the purpose E se
153. es Olympus Soft Imaging Solutions GmbH analySIS FIVE Setup Build 1210 Automatic 47 calibration Select the magnification of the TY adapter and the objective magnifications of pour Microscope Automatic calibration usina motoneed microscope etal Shela Back Cancel Please note the following points during automatic calibration Requirements for e Automatic calibration is only possible for light microscopes and certain camera automatic types calibration You can only use the automatic calibration if you do not use a magnification changer on your microscope and your microscopes tube factor is equal to 1 e In order to be able to exactly determine the end magnification of your system you must supply the magnification of your TV adapter during installation The TV adapter can be found between the microscope tube and the camera The magnification is usually shown on the TV adapter e You cannot use the automatic calibration for stereo microscopes Please note amp e You will recognize precalibrated input channels in the Set Input dialog box by the XY Calibrated extension Le Acquiring images Calibrating inputs Step by step Calibrating images Setting magnification Remote control Step by step Setting acquisition conditions Check calibration data 41 aii Color iew Ill u Fr Colorview Ulu PA y Calibrate cl e During installation provide the objectives which are to be used on
154. es 159 Classifying particles cecccccseeececeseeeeeeeeeeeeeeseeeeeeeeeaseeeeseeeeeeseeaeeeeeseeeeeeas 161 Possible stumbling blocks during a particle analysis cccseeeeeeeeeeeees 166 Report Generator assercion aaae 168 Creating TEDOS niaren a a a tia 168 Saving EXPONINO TEPO senene e E hen coaaheumeneseeaet 172 REPOT ODJECIS aana E A E ee re eee en eee 173 image OBJ SClS iiaa r e EREA 177 NOCO ODJECA a E ET 181 TOODE E e E E A E omen ee Rees 188 SECT ODJECA eA a a T 192 Diagrami ODJECE a E ATE AEA E EA 197 EDOM TEMPIALCS srecna a a a aa dttaseiubiaGiinni 197 Creating saving new templates ccccccsseecceecseeeeeeeeeeeeeeeaeeseeeeeseeeeesaaes 197 Object templates cccccccssseececeeeeeeeceeeeeeeseeceeseeuseeessaeeesseaeeesseeeeesseaass 202 Planning TEPOM TEMPIALSS aa a a 204 Step by Step analySIS Step by Step analySIS Background information Step by Step analySI S Installing analySIS Background information Welcome to analySI S analySIS configuration www olympus sis com Software protection The software is protected by a dongle On the left you can see the LPT dongle for the parallel port on the right the standard USB dongle The software package you have chosen is by Olympus Soft Imaging Solutions You have thus entered into the worldwide analySlS user community Welcome The broad range of functions for digital image acquisition image processing analysis databa
155. etail image Then pull one of the selection markers while keeping the left mouse button depressed gt The zoom level of the detail image will change according to the size of the image object The image segment being shown remains unchanged The auxiliary lines are automatically altered to fit the new position of the image segment detail image 6 Now it s time to alter the size and position of the image segment e Select the red frame delineating the image segment You can alter its size and position within the image any way you like gt After every alteration to the image segment the detail image will be changed accordingly The position of the detail image is not affected by this A zoomed image detail called Detail Zoom is comprised of the image segment the image de tail and two auxiliary lines Image object Detail image Image segment a Auxiliary lines 7 Now you format the zoomed detail e Select the detail image and click the Properties button in the Report Ob jects button bar You ll find all properties for image objects for the detail im age in the Properties tab All zoom levels and automatic labelling are avail able e Select the image segment and click the Properties button You can set col or line type and width in the Line tab e Select one of the auxiliary lines and click the Properties button You can set color line type and width in the Line tab Record objects
156. etect ed particles from the particle list gt The pointer will appear within the image 2 Leftclick on all the particles you wish to remove gt The particles are shown in another color in the overlay 3 Rightclick to confirm the particle selection gt The deleted particles are no longer shown in the overlay and no long er appear later in measurement sheets Appending particles one at a time 1 Select the Analysis gt Append Particles command to add particles to the list of detected particles gt All particles that have already been detected will appear as outlines in the image overlay for reference purposes No matter what the cur rent classification is the color of these particles is always green gt All other overlay objects will disappear from view 2 Select the Fill holes check box in the Append Particles dialog box to have inclusions holes within particles ignored Clear the Outline check box to have appended particles shown filled in in the overlay 3 Select one of 7 methods of having particles drawn within the image over lay a Click the Magic Wand button for example to have the outline of a particle n automatically calculated via the image s gray or color values gt The pointer will appear within the image window 4 Click on a gray or color value representative of that particle gt The selected point of reference will be shown as a blue point in the image overlay gt All pixels comprisi
157. ew dialog box offers 6 different displays of the database window Full View gt A table is displayed in the full view The database view selected under Table View instead of the gallery the Full View option is automatically Awi chosen by clicking the Full View Ee View gt Default full view including gallery Simon located in the Database button bar Click the Next View Full view gt The gallery is displayed as a single button to alternate between gallery Horizontal row In this way the size of the and table views Gallery View gallery section is reduced in favor of the form Narrow View The form view disappears and the gallery is reduced to a small strip Equates to the view which is selected by clicking on the Narrow view button Structure Strip Reduces the database window to the preview window and tree structure Gallery bar Reduces the database window to the gallery view Use the Superordi nate record button in this view to move within the database You will find the buttons in the database window button bar 2 Select one of the views offered and confirm by clicking OK Configuring and opening the info window 1 Select the Database gt View gt Arrange Fields command Unfold the Info Window branch in the tree structure 3 Mark the Image data type In the Available list mark the user fields that you want to display in the info window and click the Add gt gt button o e Remember that
158. f the active page template which is Report consecutive number Report container src Template container stc Report srd Report template srt The Report Template button bar is a part of the report window It differentiates itself in some functions from the button bar used for creating reports Please keep in mind that these buttons functions are not available as menu functions This is why this but ton bar should remain visible If you like you can use the Special gt Edit Button Bars command to show or hide the button bar or to add other frequently used buttons Report Generator Creating saving new templates Background information Finish Object Editing Edit Object Template Leave Page Templage Save Page Template select Page Template New Page Template save Report Template Set Zoom Redo Undo Background objects Page templates can include background objects Background objects that have been defined for a page template will appear on each report page created based on that page template Background objects cannot be edited on a report page This is why you cannot select them on a report page Text objects and all graphic objects are automatically inserted as a background ob ject in a template Image objects sheet objects diagram objects and graph objects by default are not background objects Definition Select one or more objects on a template page Open the dialog box on ob
159. faults for various measurement parameters which are offered as defaults for a measurement A circle for example is a 2D ob ject By default the area and perimeter are exported as a measurement result Please note that the measurement parameters for all tyoes of measurement objects are shown in the Selected Measurements list Only the measurement parameters which are relevant to the measured object however are shown in the tree view of the measurement display An angle value will not be exported for a 2D object You can change the sequence of the active measurement parameters The se quence defined here is adopted by the measurement display and the export sheet If the Show labels gt Measurment result option is selected in the measurement settings measuring results are also written into the overlay Here it is where you determine which parameter is displayed if you are measuring more than one parameter If you want to display measurement results in the overlay the program always shows the first measurement parameter This is how you select measurement parameters You measure 2D Objects You are interested in the area and the color of the object 1 Measure a 2D object for example with the Magic Wand measurement function 2 Click the Select Measurements button You will find the button in the measure ment display above the tree view gt The parameters are classified based on measurement types in the tree view located in the upper le
160. fication before the acquisi tion or have a scale bar automatically drawn into the image after the acquisition Online shading Optical systems consisting of camera and microscope generate image inhomogene correction ity or so called shading even if care was taken with setting up the devices The shading makes itself noticed by the fact that the image gets darker toward the edge A shading correction corrects these image flaws with the help of reference images Using the online shading correction of ColorView u these corrections already take place in the live image The online shading correction is activated in the logical input channel Before the on line shading correction is able to be used you must acquire these reference images In addition to the camera characteristics the microscope s optical characteristics es pecially the objective being used contribute to the correction image A correction im age for each camera resolution and objective combination must be made according ly A software wizard will guide you step by step through the acquisition of these refer ence images This wizard is automatically called up when you acquire the first image with the online shading correction activated Step by step Set up a new input Only set up a new input if no input has been predefined for your camera Should an input already exist it is usually better to duplicate the already existing input 1 Select the Image gt Set Input
161. field The Shadowing field is where you set the reflectivity of the model The higher the shadowing the more tangible the model will seem Select the color for your light source in the Color field O Select the Show position arrow check box Reduce the distance in the Dis tance field until the position arrow comes into view Clear the Position with navigation window check box Select the Fixed in space position The entries of the Distance Rotation X and Rotation Z fields are for moving the light source in relation to the model The 3D Navigator on the other hand is for moving the model in relation to the light source 7 Close the Rendering Settings dialog box The artificial light source makes the model surface look more tangible left You can use an arrow to in dicate the light source s po sition and then have the model illuminated from vari ous angles right Choosing a background color 1 Click the Rendering Settings button 3 D button bar along the upper edge of 3D window 2 Select the Options tab Doubleclick on the Background field and select the color desired 3 Close the Rendering Settings dialog box SEL 136 Creating 3 D surfaces Measuring models Background information Measuring models Background information Measuring 3 D models Interactive measurement functions Measurement results Deleting measurement results Warning S Step by step Interactive measur
162. for the exposure time of the live acquisition while Snap Exp Snapshot Ex posure Time stands for the exposure time of the snapshot Independent of the calculated exposure time for the snapshot the exposure time for the live acquisition cannot exceed 125 ms In this way a quickly reacting live image is guaranteed which simplifies setting the microscope while the camera is running 4 Bring the image into focus e Before you focus click the Focus mode button By doing this you will switch the camera to the highest resolution One camera pixel is then ex actly equal to one pixel on your screen Then click the Focus mode button once more to return to a view of the complete image 5 Click the White Balance button to conduct a white balance In the image win dow move the ROl s red rectangle to a white or uniformly gray position on the specimen Change the size of the ROI by keeping the mouse depressed and moving the mouse Rightclick to confirm position and size of the ROI e When using a reflected light microscope you can simply take a white sheet of paper as a sample for the white balance When using a transmitted light microscope try to find a position on the mi croscope slide without a sample 6 The Exposure adjustment slide control enables you to manually influence the exposure time for snapshots as calculated by intelligent Exposure Move the Exposure adjustment slide control to the right to increase the exposure time or to the
163. from the Select Measurements dialog box Image Manager x x a z eles D Origin Area 1063 38 nit ts Measurements of T 25 Mean Hue 195 30 Shape Factor 0 72 2D Object 2D Object 2D Object 2D Object Orientation Convex 59 03 Area Mean Hue Shape Factor Orientation Convex um i 1001 81 195 53 0 56 103 64 ee List Lal Gal F Gra lpr 1010 56 15 2 O74 Optimizing work environment for measuring Background information Magnifier Navigator Your image analysis program offers you Navigator and Magnifier to set measure ment points as accurately as possible onto large images Both settings can be found in the viewport manager Click on the last button to get a list with the possible Navi gator Magnifier and Viewports views Select the desired view e Working with Navigator View the image in the image window with a zoom factor of 100 When using a large image only a part of the image will be shown The Navigator view always shows the entire image This way you can keep an eye on things and find your way around on large images The red rectangle in Navigator shows which image section will be shown in the image window Before a measurement select a part of the image you are interested in directly in Navigator by moving the red frame onto the overview image by keeping the left mouse button depressed Interactive Image Measurement Optimizing work environment for measuring Backgro
164. ft hand part of the dialog box 3 In the tree view select the 2D Object entry to limit the measurement parameter list to the parameter for 2D objects cl 124 Interactive Image Measurement Optimizing work environment for measuring Background information There are more mea surement parameters available for interactive measurements than those shown by default 4 Mark the check box of a measurement parameter in the Measurements list to activate it for the measurement 5 For example mark the Mean Hue check box to measure the hue of a 2D object An object s hue corresponds to the mean hue of all pixels which belong to this object gt The selected parameter has now been activated for the measurement and will be shown in the Selected Measurements list below 6 In the Selected Measurements list select one of the default parameters for 2D objects e g Radius Mean Click the Delete button gt The deleted parameter has now been deactivated for the measurement It is of course available for later measurements 7 Close the Select Measurements dialog box by clicking OK gt The measurement display is updated and shows all of the active parame ters which can be used on a 2D object The sequence of the measurement parameters is adopted from the Select Measurements dialog box 8 Create a measurement sheet gt The measurement sheet contains all the active parameters The sequence of the measurement parameters is adopted
165. further data can be inserted under a document e You cannot define database fields for documents which provide further informa tion when inserting the documents e There is only a limited number of database fields which you can use to search for documents These include record names file names or insertion date and insertion time Generally you will find the documents by looking for the higher ranking record Document files Document files are data that has already been saved in a file These may also be files that cannot be loaded into your image analysis program but which belong to other application programs e g CorelDraw Excel Origin PDF AVI or Word files Inserting document You can insert document files into the database as follows files e Mark the record in the tree structure to which you want to attach the document e Click the right mouse button and select the Insert gt Document File command e Select the correct directory and mark the required files e Click the Insert button Step by step Insert documents You have created a database An image is already in the database folder Now you want to file further result documents in the database folder 1 Load the documents that you want to insert into the database folder gt Documents are diagrams texts sheets and reports 2 In the tree structure of the database window mark the database folder into which you want to insert the documents 3 Click on the right
166. g Images Create a new database folder Step by step 3 The automatically created entry Project lt ConsecutiveNo gt will be offered as the project name You can replace this entry with any other project name The database will however not accept a database folder name that has already been used in the database 4 Click the Insert button gt In the database window you will find a tree structure on lower left The uppermost entry in the tree structure is the name of the database A new project will be created as a database folder below the database name You can now insert the project data such as images graphs sheets and other documents into this database folder gt Inthe database window you will find a gallery view on the upper right The new project will be represented in the gallery by a schematic folder icon 5 Click on the newly set up project in the tree view gt In the database window you will find a form view on lower right You will now find information regarding the new project here The form shows all database fields which you have defined in the Arrange Fields dialog box for Form View and the Project data type L9 68 Archiving Images Insert data Step by step How to create a new database folder Newly set up database amp Datat ase01 apl SO BAB 7 Be aa 3 No records available Databasel1 Field value Databasef1 c 4rchive Databasel Project Choose View
167. ge layouts The report generator which is integrated into your image analysis program enables you to design a page independently You define your own standard page layout for printing out single multiple images or da tabase images and for printing out text sheets diagrams and graphs as well The illustration de scribes terms which are used in the Define Page Layout dialog box Field codes for headers footers Saving Printing E mailing Printing images Background Information Define Page Layout Header Footer Header Footer Header Footer Single Image Multiple Images Other Documents Border Freeview Fit image size to i Page borders Width height Ton 25 El Bottom 2 5 Left 2 0 Right 2 0 A Header 1 0 B Footer io is Magnification Original 766 00 576 00 Piel W Fixed image ratio Print area width fier fF Center Height fizi B W Horizontal W Vertical Magnification 002035 B 20 1 28 8 cm Print Fie OF Cancel Help Border Right Border Left Header Border To Single Image A p Header Footer Multiple images Y __Footerarea Footer Border Bottom Non printable paper area Single Image Use predefined field codes in headers and footers to have certain document proper ties or information automatically included in your documents Field codes are always introduced by the follow
168. ge resolution e Underscan the system automatically selects from the zoom factors of 25 50 100 the one at which the entire image is displayed within the viewport This may mean that some viewport space is left over e Overscan the system automatically selects from the zoom factors of 25 50 100 the lowest zoom factor at which the complete viewport is taken up by the image In certain cases the image will not be visible in its entirety e Adjust to viewport image size is adjusted to fit the viewport s current size In some cases stripes can appear in the live image display Should this be the case use either the Underscan scaling or the Overscan scaling e Full size 100 the live image will be shown with no zoom factor If the view port is smaller than the image only as much of the image as fits within the view port will be shown Acquiring images Optimizing display Step by step Depending on the im 1 Underscan 25 2 Overscan 50 F The image is completely The viewport is the image will appear in different sizes in the ps aod viewport li a 3 Adjust to viewport 30 4 4 Full size 100 Only the upper left The image size is n _ adjusted to the size of corner of the image is the viewport displayed i Step by step Optimize live display 1 Select the Image gt Configure Input command or click on the Configure Input button in the Set Input dialog box 2 Select th
169. ges down i e vertically into the Vertical field e Define the distance between images and the distance to the headers and footers in the Border group Page borders will be defined according to the Single Image tab Saving Printing E mailing E mailing images Background Information 6 Click the Print button to open the Print Image dialog box Once your have de fined the page layout one time you can simply select the File gt Print com mand for any future printouts 7 Select Multiple Images in the Page layout list in the Print Image dialog box EAE e This list also includes Single Image to have images printed out one per pe page 8 Select the All images option in the Print images group to print out all images cur rently loaded e lf your have selected the Range of images option you will need to enter the corresponding image buffer numbers into the field below this option If you enter e g 4 7 3 the images in image buffers 4 5 6 7 3 will be printed out 9 To start printing click on OK gt The number of pages printed will automatically refer to the number of im ages selected E mailing images Background Information The following is The File gt Send email command is only available if required documents are loaded e g an image and a report and e you have installed a MAPI supported e mail program and MAPI DLL file Sending Select the Add a workspace for the selected documents ch
170. gram Archiving Images Finding data Step by step Step by step Selecting the database fields which you need in the query mask In your database there is the user defined User field You want to be able to find all the images the user Mr Smith inserted into the database in 2003 1 Select the Database gt View gt Arrange Fields command 2 Mark Query by Example in the View Type list 3 Select the fields in which you want to search for images e g the user defined User field and the predefined Document Insertion Date field 4 Click OK to close the dialog box Searching for images in your database 1 Select the Database gt Query by Example command gt The Query by Example dialog box contains the selected database fields 2 Enter the required entries into one or more fields For example enter Mr Smith into the User field and 31 12 2002 into the Document Insertion Date field e During the query by example fields are linked with AND You will only find the images which fulfill all the search criteria simultaneously e The query mask offers you a selection assistant for all date fields Click the button next to the date field A dialog box with a predefined date opens Click on the arrow to open a calendar in which you can select the date that you need 3 Click the Advanced gt gt button in the query mask Click the Unselect All button Mark the check box in front of the Image data type t
171. gs have Image Analysis Defining detection area Background information 7 Define the gray value range for the first phase directly in the diagram De fine the gray value range such that all particles belonging to that phase are shown in color gt Move the mouse pointer over one of the two threshold lines The mouse pointer will change into a double arrow Hold down the left mouse button and pull the threshold to the desired value The set gray value range will be colored within the image Gray value ranges are set Histogram right in the histogram The Left Right Threshold gray value ranges of the dif ferent phases appear in col or within the image when setting thresholds Mouse Pointer Number of Pixels Color Bar Gray Values 106 140 255 8 Click the New button to add a second phase gt Anew entry will be added to the Phase list The standard name can be substituted with any other you might prefer gt The new phase will automatically be colored in a color not yet taken If you like you can alter the color by selecting one from the Color pal ette gt The newly added phase will now be activated the diagram will now show the threshold values for the new phase In the image the corre sponding gray values are displayed in color 9 Define the gray value range for the second phase 10 Confirm the new threshold setting by clicking on OK Defining detection area Background informa
172. h different text format When in text entry mode the pointer is positioned within a text object allowing you to insert text The text entry mode is active directly after a text object has been inserted If you want to edit texts in already existing text objects doubleclick the text object us Warning 5 Layout mode Text flow Insertion of text objects Text proper ties Warning 5 Grouping text objects Aligning texts Insert Auto Texts Report Generator Text objects Background information ing the left mouse key Doubleclicking does not put you in the text entry mode but instead opens the dialog box for text properties The Text tab also allows you to enter or edit text Left click on an arbitrary position outside of the text object in order to end the text entry mode and to switch to layout mode The text may have a somewhat different format in the text entry mode than in the ac tual report You can only edit the text object in the layout mode not the text itself You can alter the size of the text object by pulling at the selection markers If you alter the size of a text object you are thus altering the size of the text object not of the actual text Font type and size are not affected Multi line text automatically fits itself to the al tered size of the text object When in the text entry mode you can enter as many lines of text as you like The only lines that remain visible are those that fit
173. hat image will be overwritten Please not that the images are not automatically saved as a file Therefore you must either in sert the images into a database or save them as a file by using the File gt Save As command e Image Buffer Circular Switch Your image analysis program will now automat ically select the next image buffer before each new image is acquired Only the image buffers which belong to the current circular switch will be taken into con sideration The first 8 image buffers are by default If image buffer 8 is the active image buffer image buffer 1 is again going to be the next image buffer which is selected Every loaded image takes up space in the memory Select this option to avoid filling the image buffer with a large amount of unnecessary images e Database An acquired image is written to the active image buffer and simulta neously inserted into the active database The image is thus automatically saved as a file You do not have to additionally save acquired images with the File gt Save As command Please note The program tries to insert the acquired image beneath the active database element You will get an error message if the active database element does not allow the insertion of images Images can be saved below a database folder or an image but not directly below the database symbol or below a doc ument The insertion mask is not shown All of the user defined database fields remain empty for the ins
174. he Automatic Gain Displaylnversely there is increased noise if the image is very much underexposed You cannot use the Automatic Gain Display if you want to compare the intensities of numerous images with one another LE 32 Acquiring images Optimizing display Background information This online histogram shows a narrow distribu tion The image would thus be dark and lacking contrast without auto matic gain display When the Automatic Gain Display has been activated the existing signal range will be spread to improve mon itor display This makes image structures much more clearly visible Online histogram The histogram shows you if the image is illumi nated properly The dis tribution is cut off to the right if the image is over exposed If the image is underexposed the dis tribution shows a peak at the left Image scaling rT gt 4 Histogram x If the Online Histogram check box has been selected you can check the intensity distribution during image acquisition During image acquisition a window showing the current histogram will appear automatically This histogram will be continually up dated Histogram 00 100 0 Mir 0 0 Mean 35 14 Max 100 0 1600 4095 D ot Eee a Your image analysis program offers you several possibilities to customize the size of the image to fit the active viewport The view of the image in the viewport does not have any effect on the actual ima
175. he Gamma filter in the Filter List gt The Value field will appear in the Parameter group 601 110 Processing images Filtering RGB images Step by step Images are edited ina separate preview win dow when using the RGB Studio All opera tions applied to the im age are shown in this window immediately All overlay information and or automatic scale bar do not appear while you define filters e Use the arrow buttons next to the Value field to set the desired y constant The value range is 0 1 to 100 0 e Any alteration of the y constant is applied to the image immediately and shown in the preview window Keep making adjustments until satisfied with the results 5 To increase image sharpness select the Sharpen filter in the Filter List gt The Value field will appear in the Parameter group 6 Use the arrow buttons next to the Value field to set the sharpness desired e The value range is 1000 to 1000 Promille gt Any alteration of sharpness is applied to the image immediately and shown in the preview window Keep making adjustments until satisfied with the re sults 7 To increase image contrast select the Stretch Intensity filter in the Filter List 8 Click the Execute button gt The filter will be applied to the image and the results shown in the preview window e To reverse the Stretch Intensity filter operation use the Back button if im age contrast is still too weak or perhaps even too great Then
176. he bitmap desired and click the Open button This might be e g your company logo or a comparison im age In the installation directory of your image analysis program you will find samples of all supported file types in the Overlay subdirectory gt A rectangle the size of the bitmap will be displayed in the overlay Position the rectangle as you like and rightclick to have it transferred to the overlay 3 Click the Object Properties button to frame the bitmap or have one of its colors changed 4 Should you want to hide a color Select a color that occurs in the bitmap in the Keying color palette and then select Transparent in the Background palette 5 Click OK to close the dialog box 6 The color selected will no longer be displayed The bitmap will be transparent where the color selected had been the original image shows through Saving and reloading overlays 1 Click the Select All button gt All overlay objects will appear surrounded by selection markers E 2 To save the selected overlay objects to a file click the Save Objects button in the Overlay button bar 3 Issue a name for the overlay in the Save As dialog box and click the Save but ton gt The entire overlay consisting of text arrow and bitmap will be saved to an OVL file Editing existing overlay objects 1 Click the Edit Overlay button to alter the properties of an existing overlay object gt The mouse pointer will appear within
177. he camera controls and click the Auto button enable the exposure time to be calculated automatically Activate the automatic gain display in the camera controls This guaran tees that the acquired images will not be so dark that the calibration length is no longer recognizable when using higher magnifications e Select the Image gt Snapshot command to finish live image acquisition 2 Place a suitable calibration specimen for example a stage micrometer into your microscope and focus The sample image right shows a calibra tion scale in a light mi croscope at a magnifi cation of 20 0 10 50 60 70 8 iii Mouse Cursor Calibration Length 500 um Starting Point Final Point 3 Maximize the image window and set the zoom factor to at least 100 4 Select the Image gt Configure Input command or click on the Configure Input button of the Set Input dialog box to calibrate the current logical input channel 5 Select the XY Calibration tab Configure Input Info 9 Calibration Magnification Macro Input Display Format Magniticatiorn zo Calibrate amp calibration 0 8306 pm F Unit Y calibration 0 5306 pri Dey ey ratio fi M Fixed Acquire Calibration Snapshot ERED f Arbitrary Horizontal C Vertical Calibration length 500 Lin Cancel Help 6 Click on the Unit button e Select m for meters in the Basic unit lis
178. he destination image buffer e WARNING If you have selected a certain image area using the Image gt Set Frame command color adjustment will only be applied to the image area selected via the frame SOL 106 Processing images Filtering gray value images Background Information e To apply the same color adjustment parameters to other images simply select the Adjust Colors gt Execute RGB Adjustment command as often as needed Filtering gray value images Background Information What are filters How does a filter work What types of filters are there What filter to use for what purpose Shot noise and single defective pixels can be deleted using the medi an filter Edges remain sharp Step by step Filters are neighborhood operations a pixel s brightness in the resulting image is computed by taking into consideration the brightness of the original pixel itself as well as the brightness of its neighboring pixels also in the original image The simplest filter is the mean filter 3x3 pixels surrounding a pixel are added and di vided by 9 the number of pixels to compute the pixel s brightness in the resulting image This reduces statistical noise occurring randomly throughout the image by a factor of 3 The mean filter is a convolution filter this kind of filter is defined via a matrix the size of the pixel neighborhood e g 5x5 The numerical values of the matrix are weight ing factors w
179. he text objects simultaneously When you wish to align text objects using the functions of the Align button bar the vertical alignment of all the text objects being aligned should be the same The rea son for this is that all the functions are for the text objects not the texts themselves If you want to align text within the text frame then go to the ext tab in the text prop erties AutoTexts AutoTexts are a specific kind of text objects whose contents are independently de termined You can use AutoTexts for reports and report templates Click this button in the Report Objects button bar to insert an AutoText The Seleci Auto Text dialog box offers you all of the available AutoTexts For example Insert the AutoText called Page Number to have report pages numbered Your image analy sis program will automatically fill in the correct page number when you e g delete a page located before the current page 681 190 Report Generator Report objects Background information Different page templates Formatting text variables AutoText properties can be altered just like the properties of any other report object inthe Report Object Properties dialog box In addition to the properties to which you can assign text objects you will find the Auto l ext tab where you can decide the type of AutoText and the way AutoTexts are updated Text variables In order to change a text object to a text variable you have to alte
180. heet S61 196 Report Generator Report objects Step by step Using sheets in a record object 1 Open an image database and insert a sheet 2 Generate a new report based on the Normal template 3 Use the Record button in the Report Objects button bar to insert an existing record object 4 Click the Edit Object Template in the report window button bar to switch over to m the edit object mode 5 Select the image object and click the Sheet button located in the Report Objects button bar and pull open the sheet object 6 Click the Properties button in the Report Objects button bar 7 Inthe Document Link tab enter the Filename into the field in order to insert the first attached sheet together with the record Determine the number of rows and columns which are to be inserted into the report The heading of a measurement sheet usually has the sheet cell number 0 Please note If you use 0 as the amount of rows or columns your image analysis program inserts exactly that part of the sheet which was active during the inser tion of the sheets into the database 8 Click OK to close the dialog box 9 Click the Finish Object Editing button in the report window button bar to exit the edit object mode 10 Now insert the sheet from the database into the adapted record object To do SO you Can either move the sheet or also the record under which the sheet has been inserted onto the record object gt The sheet an
181. hich are multiplied with the corresponding neighboring pixels The mean filter e g uses a 3x3 matrix of values of 1 Another class of filters are the rank order filters The median filter is one for example This involves sorting all the neighboring pixels according to brightness The original pixel is then replaced with the median pixel of this ranking order This filter is used to correct shot noise and single defective pixels e correcting statistical noise NXN Mean Sigma Lowpass Rank e correcting shot noise and defective pixels Median Rank e enhancing contrast accentuating image detail Sharpen Sharpen II DCE e accentuating edges Laplace Sobel Roberts and others Suppressing noise 1 Load the image or activate the image buffer and set the destination image buff er 2 Select the Oper gt Filter gt Mean command to average out statistical noise gt The filtered image will be written into the destination image buffer 3 Activate the original image Set a different destination image buffer 4 Select the Oper gt Define Filter gt NxN command to define how much the im age is be averaged Statistical noise can be suppressed using vari ous filters Mean upper right NxN iterations 1 and size 5 lower left Lowpass lower right In the filtered images the basic structure with in the image becomes apparent Processing images Filtering gray value images Step by step gt The Define
182. hown in the image window directly in the overview image located in the navigator Rightclick in the viewport manager to open the context menu Select the Show Live command to view the live image in the navigator The magnifier shows a magnified portion of the image in the active image buffer Move the pointer across the image The shown section always corresponds to the image sec tion which is directly under the pointer Rightclick in the viewpoint manager to set the zoom factor of the magnified image Viewport M anager E Viewport M anager ES iewport M anager 1 Neurons5 Navigator Magnifier Navigator Viewports L Yiewpits This paragraph is only relevant if your system supports two monitors A dual screen system means that there is an additional monitor which is exclusively used for view ing images The Windows monitor is the main monitor on which your operating sys tem runs The second monitor is called the dual monitor The dual monitor solely con tains an additional image window The viewport manager contains a tab for each monitor Click on the appropriate tab to switch back and forth between the monitors Use the buttons located in the view port manager to influence the appearance of the dual monitor Optimizing display 1 Press Ctrl Alt T to generate a test image e The image window contains a button bar with which you can quickly alter the appearance of the images in the image window 6L
183. ia coordinate transformation The HSI model is easier to understand than the RGB model because its parameters are more in line with one s own intuitive description of a color Saturation cyan white black col 104 Processing images Adjusting image color Background Information Gamma correction Define RGB Adjustment Intensity Adjustment The gamma brightness and contrast parame ters have been adjusted in the above image ar eas left Gamma gt 1 means the image is brightened and contrast in dark im age areas is increased center Brightness 200 means that in tensity is increased Color values remain constant right Contrast 1000 mainly raises color satu ration Color values re main unchanged Gamma correction increases or reduces image contrast selectively dependent on in tensity values E A where I R is the intensity value of the resulting image I O the intensity value of the original image A y lt 1 gamma value darkens the image as a whole Contrast of bright image areas is increased A y gt 1 gamma value brightens the image as a whole Contrast of dark image areas is increased A y lt 1 gamma value does not change the image in any way The Oper menu has a submenu called Adjust Colors containing commands for cor recting false color and intensity within images The different commands function the same way in principle For example the Oper gt Adjust Color gt D
184. ialog box for loading images also has a preview func tion The Files of type list is in all dialog boxes for load ing documents It pro vides file formats for all document types 16 Loading images stored on the hard drive 1 Click on the image buffer you wish to load the image into with the left mouse button in the Image Manager Activate for example image buffer 5 gt The image buffer selected will be color highlighted and assigned to the ac tive viewport 2 Select the File gt Open command to load an image gt The Open Image dialog box will appear Open Image EES Look in E Images E c FE A i F Skin tif F Steel tif F woudl tif a E A File name Aulabel ti Files of type Tagged Image Format tif Cancel 3 Select Tagged Image Format tif the standard image format in the Files of type list e This format is the default when you open this dialog box for the first time Files of type Database mdb Cancel Database mobi Database f mdb Help Module Formats Al f 4 Click the Up One Level button to move up a level in the directory structure of your computer gt Inthe field below the button bar you will find a list of all sub folders and doc uments of the file types selected 5 Doubleclick on one of the folders listed to get a listing of its contents i e all sub directories and files the folder contains e The root
185. ication currently set on your microscope and then click on OK e You may also enter magnifications not on the list Your image analysis pro gram will then use interpolation to ensure that the image calibration is cor rect Acquire an image 5 Select the Image gt Acquisition command to display the camera image live on screen gt As long as live acquisition is ongoing the camera icon blinks in the status bar and the input channel name will be red gt The live image will be shown in the active viewport e The size of the image within the viewport will depend on what you have se lected on the Image scaling setting on the Display tab Image gt Configure Input 6 Optimize illumination position and focus of the object in the microscope 7 Select the Image gt Camera Control command to optimize acquisition quality by adjusting exposure time as well as color brightness contrast and focus set tings e Close the Set Input dialog box because otherwise the Camera Control command will not be available e The functionality of the Camera Contro dialog box will depend on what kind of camera you are using 8 Select the Image gt Snapshot command to finish live image acquisition gt The image will be written into the active image buffer Now it may be edited evaluated and archived gt The image is given a standard name This name is determined by the Pre fix for images and Incremental number settings in the Image tab
186. icking on OK 23 Once again set the acquisition parameters which you use as default for image acquisition Check calibration data Even when you are using a precalibrated input check the calibration data 1 Display a calibration object with your microscope for example a stage microme ter with a total length of 1 mm 2 Select the Image gt Set Input command Select the input which you would like to check 3 Select the Image gt Set Magnification command Select the current magnifica tion 4 Select the Image gt Acquire command to acquire an image of the calibration ob ject 5 Use the key stroke Alt 4 or click the Measurements Bar button to show the but ton bar with interactive measurement functions 6 For example click the Arbitrary Line button gt The pointer jumps into the image IEEE e 7 Measure the length of a segment on the scale Using the left mouse button click once on the starting and endpoints of the segment to be measured Click the right mouse button to return to the user interface gt The length of the segment to be measured is shown in the image overlay Should the measurement result not correspond with the actual length of the segment you must calibrate the input again Saving images Background information Image name The image name is the name of the image in the image buffer This name is not nec essarily the same as the file name or the image record name of the image in th
187. ies for data storage ccccccseesceeeseeeeeeeeeeeeeeeeeeeeesaaeeeeeeas 57 Sel Up a NEW CalabaSes seis ct tats Coe ea eae thease a teats 58 Define organizational fields ccccseescecceseeeeeceeeseeeceeeeeessueseeesseneeeessaaeeess 63 Define database fields vsccxcicccdaccas satat race cuavcenewogeahentaa eia Enare iaeei 63 SERVO aeran aaa ned eatexauerie Midyear E 66 Create a new database folder cceccccccccesseeeeceeeeeseeeeeeeseeeeeeeeseeeeeeeeeeesaas 66 HIS CM IMAG CS varcnuntiec ie Nini cntveis r iat dseauies 73 HSS He COC IANS IMS tera 2 ates oases a a aeeeaiea ee 73 Work in the database WINKOW cccccccssseeccceeeeceecaeseeeeaaeeeecseaeceeseegseeessaaeeessaageees 81 Arange hc pee eee nee OT ne ee ee 76 CHOOSE VIEW ote ee cesta a thatch satan nest read a cab duadaies 79 ELE EE r Ure Meter E tt er eta tr ser A tear errant eee renter ne E ere enna ee 84 Load Cael rst a a a R E AE ss edencssaacene 86 Arene Cae eee E a A a e a a 89 Protect with a password ersen e e amma E tude N AEE ai 94 Processing IMageS esi ciciceescs ccs tecwsncusestdssccckdecesncsmancesececedneusaswestetesenesenewae 96 EGNING OV CHAY asa a a acelin don sin lok dnioaiepbonsanan area tannialaimnraaiad 96 increasing IMAGE Contrast creea a ie weld E tal 101 Adjusting image color eeeccccseeceeeeeeeeeeeeaeeeeecaeeeeeeeeeeeeeesaeaseeeseaeeeeesaaeeeeeeaeeeeesaees 103 Fiterng gray value Images miisi e t E E 106 PING
188. ilter matrix at 50 e Should you be working with true color images select the Polynomial fit command 8 Click the Execute button to apply shading correction to the image gt The corrected image will be written into the destination image buffer e You have thus also defined parameters for further shading correc tions Simply select the Oper gt Shading Correction command to con duct them K g iii i J Pee B a a ba wi J D m E ag g 7 r roa Beek a a e ae intensity profile intensity profile gray value gray value coordinate coordinate Separating particles automatically 1 Set the zoom level of the image in the viewport to 100 2 Select the Oper gt Define Filter Separator command 3 Select the Step option in the Boundary shape group e The particle separator can also be used to track bright or dark lines Select the Dark or Bright option in this case 4 Set both Smooth and Fine Coarse slide controls to 1 et L 144 Image Analysis Detecting particles Step by step The separator calculates a separation line between gray value phases Artifacts will occur on the borders and also around holes within the particles These errors can be corrected interactive ly 5 Switch on the preview to be able to observe how adjusting settings alters the image 6 Move the Fine Coarse slide control incrementally higher until you have found the optimal setting gt If an image has a lot of
189. image 4 Click on the List or Gallery tabs located in the image manager to show the im age buffer with the loaded images U1 Load the image to be measured from the image manager Measure the desired segments N Repeat the last two steps for all the images on which you would like to make measurements 00 Click on the Create Measurement Sheet button located in the measurement button bar gt The Create Measurement Sheet dialog box opens Create Measurement Sheet x Select the images whose measurements will be included in the sheet J ie Measurements Mil Image Name Line po Length ppm Image E T 2 Imagedl O 3 Imagele 4 Imageds Cancel Select All Unselect All I Show image name in the First column riage HEE Help IY Show measurement ID 3 acka A Images Generate statistics of the sheet s 5 Images One sheet per image 6 Images Create separate column For each type of measurement 4 9 Inthe Create Measurement Sheet dialog box click the Select All button to export the measurement results for all images Select Mark the Show image name in the first column check box to additionally acquire the names of the images in addition to the values into the sheet You can thus match the individual measurement values in the export sheet clearly to an image when using numerous images This is how you delete single measurement values 114 Create sheet 119 ZL 118 Interac
190. image database into a record object When inserting the image into the record object all image entries belonging to an image can be automatically included in the report Use record objects to have report cre ation based on existing image databases largely automated Your image analysis program recognizes whether or not an image in the image man ager has been loaded from an image database You can insert this image directly from the image manager to a report whereby all of the database fields are correctly filled in Use this possibility to edit an image before inserting an image for better print results For example you can correct a tinge or conduct a sharpen filter on the image Record objects are complex report objects comprised of several separate compo nent objects Record objects usually consist of at least one image object and several field objects You can however make use of all other kinds of report objects within record objects text AutoText images and graphic elements Placeholders for text and more images are not permissible Sheets and diagrams in contrast serve as placeholders for documents which are stored below an image within the database Report Generator Record objects Background information Record object structure see sheet on facing page field objects 5 can only be used within record objects They are usually comprised of the RASS SS field name and field en SSS NS WQS try Variously formatted Pees N
191. image object If you have the magnification or the scale shown the print size of the image will be less than that of the image object The image size is the actual size of the image It is determined by image calibration An image that is 500 pixels in width and calibrated at 0 5 um pixel has an absolute image width of 500x0 5 um 250 um Your image analysis program determines absolute im age size via image information The report generator enables images to be rotated 90 Rightclick in a report window You will find the Rotate button bar under the Button Bars command Mark the image object and select one of the two buttons to rotate an image 90 clockwise or counter clockwise Fit image into the frame Use optimized magnifications oe a0 50 60 U 30 40 50 60 70 80 uu v io 100 1 4 hi 50 wm Use fixed magnification Use fixed magnification Step by step Report Generator Image Objects Step by step Inserting images from the image manager into a report 1 Load the images that you want inserted into the report into the image manager 2 Press F8 to open the Preferences dialog box and select the Report tab 3 You ll be making two fundamental decisions concerning how images are treated in the report in the Image group e Create image copies you decide whether images are to be saved along with the report or whether you d rather insert them as a link to an existing image file e Use thumbnails instead of
192. ined Folder 1 database folder You can set up further database folders for document storage at any time Template You adopt the structure from a template model or an existing database the organizational ID is the order number All documents which are entered into the database must be allocated to the relevant database folder with the order number User You define the organizational ID and the required database fields in the data defined base The organizational ID is the central field of your database and may not be altered later for existing databases In an orders database for example Set up a new database A software wizard guides you step by step through the setting up of the database 1 Select the Database gt Administration gt New Database command 2 Enter the name of your database into the Database name field gt The software wizard suggests an identically named subfolder in the data base directory for the storage of the database files Even if you change the suggested directory you should still set up a separate directory for each database 3 Click the Next gt button 4 Confirm the question as to whether the database directory should be set up 5 Select the User defined option Click the Next gt button 6 Enter for example Project as the descriptive term for the organization of your documents All data that you enter into the database must be then allocated to a project folder gt Y
193. ing new templates Background information Report templates Report templates are a kind of report file in which you determine what your future re ports are to look like Each report you create using report generator is based on a report template Component parts of A report template consists of page templates and object templates These are gen a report template erated within a particular report template and are not available for use in other report templates You cannot import page or object templates from other report templates You can of course modify existing report templates and save them under a different name This way you can use all previously defined templates for your new report template What are report Report templates determine what the reports based on them look like Defining report templates for templates is thus of quintessential importance as far as creating your own reports is concerned The work you invest initially creating a well thought out report template will pay off You ll save time when you get down to actually creating reports with that template Z6L 198 Report Generator Report templates Background information Altering existing re port templates Altering templates within reports The report template left contains three dif ferent page layouts in the example The report right consists of four successive pages The 1lmagePage is the only page template that was used of those
194. ing overlay Background Information annotation layer _ d The Overlay Button Bar button shows hides the Overlay button bar You will find the button in the standard button bar The entire range of overlay functions is available via this button bar only It contains a broad variety of tools for making your overlay as you like it Button Edit Overlay Select All Select None description switches you into the edit object mode for overlay objects The edit object mode is for selecting moving and editing overlay objects This button is only available if at least one overlay object is present selects all overlay objects in the active image This button is only available if no objects have been selected in the overlay cancels all current selections This button is only available if overlay objects have been selected Object Proper is for setting object properties The properties which are avail ties able will depend on the type of overlay object selected Burn Overlay ayers opens a multiple function submenu for dealing with overlay You can make overlay layers appear or disappear Overlay layers containing automatically generated measurement data can be protected from unintentional alterations writes the overlay of the active image buffer irreversibly into the image All image information beneath the overlay will be overwritten Delete Layers deletes all objects of the overlay la
195. ing symbol They are placed in curved brackets To have an image s name printed out along with the image you would enter the following Name Field codes in headers footers Name Comment Buf image creation date Page Copy PrintMag Date LS 52 Saving Printing E mailing Printing images Step by step Time time of image creation Now time at printout Context sensitive The File gt Print command is context sensitive and thus dependent on what kind of print settings document is active If the active document is an image the Print Image dialog box will be opened Different document types open respectively different dialog boxes Print Directly Click the Print Directly button in the Standard button bar to print out the active docu 5 ment without having to go through a dialog box The active page layout will be used when you print directly Draft mode The draft mode is for trial printouts Gray rectangles will appear at images positions and header and footer dimensions will also be indicated via rectangles The actual images will not be printed out as image prints can be time consuming Draft mode printing is a fast and easy way to check out how your layout looks e g when you just want to see what images exact positions look like on a form Step by step Defining multiple image page layouts for printing out 1 Select the File gt Define Page Layout command 2 Select th
196. input channel will be opened 2 Select the Macro tab 3 Enter the function name of the command desired into the Postprocessing steps field and put a semicolon at the end of the line SetMagnification 4 Test the little macro To do so click the Execute button e lf you receive an error message then check your spelling of the command name e Ifthe Set Magnification dialog box is opened your macro functions correct ly Then click on OK 5 Select the Enabled check box 6 Exit the Configure Input dialog box via OK 7 To test the input channel click the Snapshot button in the Standard button bar gt Your image analysis program will open the Set Magnification dialog box af ter image acquisition Showing scale bars Background information Automatic scale bar You can show scale bars in the viewport These show you the calibration of the im age s continuously as you work no matter what the viewport settings are Scale bars and Your image analysis program computes the length of the scale bar based on current image calibration image calibration Make sure that your images are always correctly calibrated e Images you acquire via your image analysis program will automatically be cor rectly calibrated as long as the logical input you re using is calibrated properly and the actual magnification is set e When working with images you import from another application or read in via the TWAIN interface be sure to use the Image gt
197. is is how you set up a new input 27 Insert into a database Document files 73 Images 70 Installation 6 network dongle 8 PDF documentation 9 Software 6 Installing the network dongle 8 Intensity Filter RGB Studio 109 Interactive measuring Measuring distances and areas 112 This is how you delete single measure ment values 114 This is how you measure numerous imag es 117 To acquire a new image with a camera for each measurement 118 To define an object with the magic wand 121 To delete an entire measurement 115 To identify a measurement on the image 115 To measure in Full Screen mode 127 To select measurement parameters 123 To work with the statistics functions 119 intX 25 Acquiring images using intX 26 Exposure time correction 26 202 208 Index White balance 26 Invert Filter RGB Studio 109 L Link to image interactive measurement 115 Live overlay 31 Live acquisition mode 34 Load Images 16 Workspaces 24 Magic wand Interactive measurement 120 Magic Wand Particle Detection 159 Magnification table 40 Magnifier 19 124 Mask 148 Maximize Contrast 101 Measurement button bar 112 Measurement Display 113 Defining statistics 119 Delete Measurement 115 Link to image 115 Measurement Settings 125 Selecting measurement parameters 122 Statistic display 119 Measurement Environment 111 Measurement Settings 125 Menu bar 12 Microscope Control Panel 38 Modify Gray Values 102 Mosaic Filter RGB Studio 109 N Navig
198. istogram calculation Full image bd Cancel Help If the Live overlay check box has been selected image overlays are also available to you in the live acquisition mode This means you may e conduct numerous measurements within a live image as well and have the re sults written in the overlay e have a measurement grid and automatic scale bar shown within the live image e during the live acquisition already highlight and label image details or more generally write texts or insert graphics into the overlay Please note The following functions for Olympus Soft Imaging Solutions cameras are available only if the Live Overlay has been activated setting the ROI for white balance in the live image Partial Readout and setting the ROI for a sharpness monitor in the live image Use the automatic gain display to acquire images independent of the illumination pa rameters The system analyze the current histogram in real time and spreads the his togram onto the entire dynamic range of the camera Even when working with the automatic gain display you should align the exposure time with the actual illumination parameters Use the online histogram as a check The exposure time should be set in such a way so that the spread of the histogram is aS wide as possible thus filling the entire dynamic range Please note The automatic gain display only slightly improves the image contrasts Over exposure cannot be corrected by t
199. j Set Default User Held valves Insert Gow Record gad Document Images lioad with Documents Image File A Data Databasel1 Arrange Fields Documents Bopp lane Document File Settings Define Contest Menu The insert mask for setting up a new project The project name can be issued automatically Insert Project Fields 1 2 The organizational fields needed for project description Project No iB Project 2 ip i Ft Cancel Help at i amp Database01_apl gt Ci S Ee a Ai EIEEE Databasel1 Prfect 2 BED atabasel1 ap Fielgfame Field value Ca Project 2 Name Database 1 Vath c Archive D atabase01 Database01 apl Created 27 02 2007 17 10 44 Last access 27 02 2007 17 23 31 Modified 27 02 2007 17 23 31 Opened exclusively yes Read only no Database identifier 6C50 185 Converted from mdb no Database version 2 03 102 Database f Set 1 OkB Z y A new project is set up Archiving Images Insert Images Background Information Changing the standard name for a new database folder 1 Open the database exclusively e Select the Database gt Open command In the Open Database dialog box select the apl file and mark the Exclusive check box 2 Select the Database gt Administration gt Settings command 3 Replace the organizatio
200. ject prop erties Objects you have selected can be changed to background objects in the Se lect and Move tab Background image If you do use an image object as a background object then you should always insert objects the image as a link Otherwise the image will be resaved for each newly created re port Altering background Use the Edit Page Template button to alter page templates within a report Any objects within a changes made to background objects will immediately affect all currently existing re report port pages Any changes you make to objects that are not background objects will only affect newly created report pages Page templates The separate pages of a report template are called page templates They re used to define page layouts that you can use later on in a report Each page layout is saved under a separate name in the report template When you subsequently create a re port based on that report template you can select a page template from the list for each report page The empty page template is a standard component of every report template Please note that it is not possible to define objects on this empty page template After sav ing the report template your image analysis program will delete this page template You can however make good use of this page for editing record objects because there are no other report objects that could interfere with your editing When you are creating an object template or
201. lect a point of reference within the image representative of the gray or color value of the image structure of interest Use tolerance to set particle thresholds When using the magic wand there are three buttons for determining the color space for true color images via tolerance definition The tolerance value is added to subtracted from the respective R G and B val ues in the RGB color space The tolerance value is added to subtracted from the respective H S and values in the HSI color space The tolerance value is added to subtracted from the H value of the original im age in the color space called Color Magic wand The magic wand is for setting different thresholds at different positions within the my 6S 160 Image Analysis Detecting particles Step by step The figures demonstrate how color space affects de tection using the magic R wand tolerance and points of reference were the same for all three detections from particles use the magic wand to define the image area you re interested in as a particle To include this particle in detection as an ROI derive the ROI from the defined particle in the Define ROIs dialog box Then you define the thresholds for actual particle detection using the ROI search area Deriving ROIs This is how you define ROIs using the magic wand before conducting detection Step by step Deleting Particles 1 Select the Analysis gt Delete Particles command to remove falsely d
202. left to shorten it 7 Click the Snapshot button to acquire a single image gt intelligent Exposure acquires a snapshot and writes it to the active image buffer The snapshot acquisition ends the live mode Configuring inputs Background information Logical input channel Your image analysis program uses the concept of logical input channels when ac quiring images via camera slowscan interface or other acquisition devices A logical input channel includes all settings relevant to image acquisition The graphical user interface of a logical input channel is basically the same for physically different ac Acquiring images Configuring inputs Step by step quisition devices such as digital cameras or video cameras The only differences are in the available functions in the Configure Input dialog box and the Camera con trol Usually the setup program installs the appropriate input channel so that you can start acquiring images immediately after installation You only then have to configure the input channel when you want to use special camera settings In the input channel you can among other things set the following aquisition parameters e the image resolution e calibration data e live image display within viewport e real time functions such as the live overlay or an over exposure warning and e macro commands to be carried out either before or after image acquisition You can for example select the microscope magni
203. ll be opened gt Your image analysis program will propose the report directory called C Reports ProjectXYZ in the Save in list 5 Enter a content relevant name for your report into the File name field 6 Select the report container src from the Save as type list to save the report in a single file 7 Click Save to save the report Saving Exporting report Background information Rich Text Format Step by step The RTF format enables you to transfer formatted text documents between various programs that can be run on various platforms You can save reports in an RTF for mat and then e g load and edit them in MS Word e RTF reports are optimized for MS Word MS Word versions 97 and later i e the report s layout remains unchanged when loaded into MS Word e RTF reports cannot be reimported into your image analysis program e Images are always inserted into an RTF file as copies and not as links This is always the case no matter how the images were inserted into the original report e MS Word can only display RTF files which can be edited in the layout or online layout view Exporting reports You want to send a report e g by e mail to fellow colleagues that have no access to your image analysis program or to the image files involved In order to do this you need a single complete file that contains all data necessary to the report 1 Select the File gt Report gt Export RTF command 2 Click
204. ll have no trouble recognizing which page template is which when inserting a new report page s Labelling text placeholders A user should be able to immediately recognize and without having to try out each blank space which report template text fields are to be filled out and which ones are background objects You should thus label each text objects of a report that is meant to be filled out by the user right from the start in the report template You can e g place text variables within square brackets and write a request in text placeholders Do not define any text fields within your templates that contain no text The user will have difficulty relocating these text fields within the templates You can t tell whether a text object is AutoText background text a text variable or editable text by simply looking at it This is why its a good idea to decide on some kind of indicator to help you more quickly distinguish between different types of text If you have several users making use of the same templates all of them should be able to tell which text objects have to be filled out and which do not You could use e g square brackets to indicate text variables in your report templates Editable text could be indicated by three dots or you can actually write a clear request within the text object Enter image comment here Configuring the Graphical User Interface GUI Take the time to configure the Graphical User Interface optimally
205. lled Client stands for all computers which are part of the network and which must be connected to the server in order to install and operate an analySIS version 1 First install the license manager on the server The license manager is required for the operation of the network dongle 2 Plug in the dongle on the computer which is to be the server and start the setup program from the analySIS CD 3 Select the Network software protection key option in the setup menu 4 In the Installation type dialog box select the Service option gt The license manager is installed after a few standard questions have been answered gt The installation of the dongle has then been completed You don t have to install an analySIS version on the server gt You don t need to copy the license manager onto any client PC To enable analySIS_ To make a quick and reliable access to the license manager possible you should to locate the license copy the nethasp ini file onto every single client PC The nethasp ini file uses the manager more server s IP address How you find out this IP address and how you use the quickly nethasp ini file will be described in the following Display the server s To find out the server s IP address when using the Windows operating system do IP address the following 1 Click the Windows Start button on the PC into which you ve inserted the network dongle and installed the license manager on 2 Select the Run co
206. load the model or activate the 3D window Then load activate the measurement sheet and se lect the Measure gt 3D Measurements gt Show Measurement Results command Image Analysis Phase analysis Background information Image Analysis Phase analysis Background information Phase analysis False color display The order is important RGB and HSI color space Step by step Phase analysis will be con ducted on a gray value im age as an example but is equally applicable to true color images as well The di alog box for setting thresh olds will look a little different that s all Ej Phase analysis is a quantitative evaluation of area with regard to each separate gray value or color phase The definition of numerous gray value or color ranges which are assigned to individual phases is a prerequisite False color display is the visualization of gray value images using colors that have nothing to do with what the actual object s colors might be False color dis play means that each gray value or entire gray value range is assigned to a cer tain color When you see a color palette in the image monitor icon in the image buffer box you know the image is a false color image Normally you begin by conducting phase analysis Measure gt Phase Analysis and then color coding Measure gt Phase Color Coding If you conduct color coding before phase analysis you will have to reactivate the image buffer con
207. lose the two dialog boxes by clicking OK Duplicate already existing input If you want to configure the input differently first duplicate one of the already existing ees In doing so you retain all of the channels settings Select the Image gt Set Input command gt All current logical input channels are listed in the Set Input dialog box 2 Choose one of the existing inputs for example the ColorView lllu FW input if you have installed a CCD color camera of the type ColorView lu Click the Duplicate channel button Ei gt The selected input channel is copied together with its settings and a new input channel is set up with these settings The number 1 is added to the name of the input Configure inputs 1 Select the Image gt Set Input command Select an already existing input 2 Click the Configure Input button to define the properties of this input channel gt The Configure Input dialog box will be opened Doubleclicking on the camera icon in the sta Colotview IT u Fw NE tus bar will open up the Configure Input dialog 3 Click on the Info tab to change the name of the input channel box also 4 Click on the Input tab to set image acquisition parameters i e The functionality of this tab will depend on what kind of camera you are us ing This may mean that your Input tab is significantly different to the one described here Acquiring images Configuring inputs Step by step 5
208. m puted by interpolation 6 Observe how the mesh size of the grid increases and decreases parallel to your increasing and decreasing step width 7 Now clear the Display as grid check box 8 Close the Modify 3D Surface dialog box Step width determines how detailed and how smooth the surface of the model is displayed Too much image information may interfere with display of the model surface above step width of 5 below step width of 20 Creating a model of an image segment 1 Click the Modify 3D Surface button Surface button bar at the lower edge of the 3D window 2 Click the ROI button to create a model based on a rectangular segment of the height map gt The image window containing the height map will be activated Define the image segment desired using the red frame e This is how you can cut out a particular surface structure or clip dark or light image edges 3 Close the Modify 3D Surface dialog box Creating 3 D surfaces Coloring models Background information Use ROIs or masks to dis play the desired segment of the height map as a model Coloring models Background information Coloring 3 D models You determine the color and shading of the model via various settings e Encoding The following can be used for coloring your model height information a texture image height image intensity values or single color display e Lighting up your model Turn on the artificial light You c
209. mages into the image manager in the order selected 2 9 G1Gl Bi el lel alal ExampleD ataba e apl re e a oe T 3 e a ih e SetDesutUsen ked Values Insert b Goto Record Skorodit La Lied tarth Wocunents Arrange Fields rt Toda E ara Bole vew Potion the Define Context Menu Loading all the data within a database folder 1 Mark a database folder in the tree structure 2 Select the Database gt Load Document with Subdocuments command if you want to load all the records within the database folder gt Images will be loaded one after another into the successive image buffers of the image buffer box gt Documents are opened in your image analysis program these are for example the sheets with the SFS file name extension and the diagrams with the SFD file name extension gt Other document files are loaded in the appropriate application programs these are for example the text files with the DOC file name extension in Word and the sheets with the XLS file name extension in Excel There are four images in the marked database folder Select the Load with Documents command to load all the images into the image manager stereo images a E Water C3 Filtering C Farticle ExampleD atabase apl gt a O lE Ga ExampleD atabate apl 3 Extended Acquisiti 9 Multiple Image Alig Phase analysis EH TEM acquisition
210. ment display You can hide or show the statistic values by clicking on the Show hide Sta tistics button located in the measurement display The name for the Statistics for group is dynamic and it shows the measurement value to which the statistics are displayed Should numerous values e g area pe rimeter and mean radius be measured in a measurement method click on one of the measurement values in the measurement display to show the statistics data of the selected measurement value instead The Statistics on all images check box is marked and is a default setting For this rea son the measurement values of the measured images contribute to the statistics Clear the check box to view only the statistics of one image Please note that this check box only deals with export to the measurement display and not with the export to a sheet Statistics for Length Count BU Mean 380 85 mm Minimum 55 mm Masimum TAF mm Standard Deviation 156 07 mm W Statistics on all images Your image analysis program offers a wide range of statistic parameters Click the Define Statistics button in the measurement display to select parameters which are relevant for measuring Only the selected parameters appear in the measurement display and in the statistics sheet You can always export the statistics of measured values to a sheet In doing so you determine which images are to be considered for the statistics in a separate dialog box The s
211. ment sheet now only contains the particles which are lo cated within the defined particle parameter Identifying particles that have specific values 1 Select a column of the results sheet and rightclick 2 Select the Sort Descending command in the context menu to have mea surement results sorted according to their numeric value 3 Doubleclick on the line number of the first line in the sheet to locate the par ticle within the image that has the greatest measurement value gt That particle will start blinking in the overlay 4 Select the Analysis gt Particle Sheet Link command gt The pointer will appear within the image window 5 Leftclick on various particles one at a time gt The sheet lines with the results of these particles will appear selected 6 Rightclick to end the Particle Sheet link ZSt Image Analysis Detecting particles Step by step The values of the current re sults sheet are linked to the particles in the overlay Have particles of a specific value range shown in the overlay The selected parti cle is particle number 25 The particle s area is ca 95 m The particle s average gray value is 152 The parti cle is within the Bright phase 158 The Feret Max parameter shows the particle contour and the tangents which are relevant for the parameter s calculation 155 18 Bright Pai 148 31 Bright Pa 154 48 Bright Pa B WR on KENG nea OT TET Pat 153 05 Brigh
212. miisg important MEOTEN ion moon your amily tem to Lhe support Leas ar Soft Imaging Syoces i De PET i Email ertachanit Ve LL 12 First Steps First Steps Background information First Steps The GUI User Interface Background information GUI Menu bar Image buffer box Active image buffer Button bars Viewport manager Image manager The graphical user interface influences the appearance of a program It determines which menus there are how the individual functions can be called up how and where files e g images are displayed and much more This chapter describes the basic elements of GUI Please note The Graphical User Interface GUI in your image analysis program is fully adaptable to meet your own specific requirements Many commands are accessible via the relevant menus You can configure the menu bar as needed Use the Special gt Define Menu Bar command to add alter or re move menus as you wish Each image is allotted its own image buffer within your image analysis program When you start up your image analysis program all available image buffers will be empty While using the program they get filled by loading or acquiring images and by performing various image operations for altering the image such that a new image results During any given work session this means that many images are accessible simultaneously Only one image buffer however may be active at a time e The image
213. mmand 3 Enter Command and confirm with OK 4 Enter the command ipconfig in the command window and confirm with the En ter key gt The IP address belonging to this computer will be shown in the command window 5 Copy the IP address you ve found to your Windows clipboard Inserting the 1 Select the Explore this CD option in the analySIS setup menu nethasp ini file You will find the nethasp ini text file in the program HASP Network Help di rectory 2 Make a backup copy of this file Open the copy you ve created 3 Replace the entry 127 0 0 1 in this file with the contents of your Windows clip board 4 Save the modified file under the name nethasp ini gt Inthe modified nethasp ini file the IP address you found for your server will then appear on the NH_SERVER_ADDR line 5 Copy the modified nethasp ini file to the Windows directory c winnt or c windows of all of the PCs that have been installed in the network on which analySIS versions run gt By employing this adapted nethasp ini file you make the search for the license manager in the complete network much easier Starting analySIS on every single client PC will take place more quickly Step by Step analySIS Any questions or problems Background information Installing analySIS Is analySIS to run on the PC on which the license manager has also been installed on the server the following step will have to additionally be taken Cop
214. mouse button to open a context menu Select the Insert gt Documents command gt The Insert Documents dialog box lists all loaded documents The check boxes in front of the documents are marked 4 Clear the check box of a document if you do not want to insert the relevant docu ment 5 Mark the Prompt for file names check box 6 Confirm the document selection by clicking OK gt The insertion mask for documents opens In contrast to the insertion of images you cannot define database fields for documents The insertion mask therefore contains only limited information about the document and an input field for the file name 7 Check the file names in the File name field If necessary change the document names eZ 74 Archiving Images Insert data Step by step gt Documents are saved in the file format in which they are normally stored in your image analysis program This ensures that all documents can be reloaded into the image analysis software If you want to save a document in another format enter the required file name extension in the File name field e g mage bmp to save an image as a bitmap or Tab xls to save a sheet as an Excel file gt The current document title will be suggested as the file name together with the standard file format which would mean for example Tab2 for a sheet 8 Click the Insert button gt The document will be saved and the insertion mask opened for the next document rep
215. n Germany ESbS51007 Olympus Soft Imaging Solutions GmbH Johann Krane Weg 39 D 48149 Munster Phone 49 251 79800 0 Fax 49 251 79800 6060 Step DY Step ANALY SUS eiwsececcus saccade cebuscacessoaeesaswinnasndeahabcaccaausiaeecexstseawaneene 5 Installing analySlIS ee 5 ANY gUesStoNnS OrProDIEMS 2 aiae A A O 9 FISI SlCDS ninan a a aa a 12 THELGUNUSerinteriaC E sites eerie a a ela eek iat aie 12 Loading images setae lotta auc a a A ee batusea dee Gn cane ne 14 Displaying multiple images cccccccesececeesecceseeceeeeecsececsseeecueeeseueeesseeeseueeessaees 18 Saving GUI configuration 2 0 eee e cece cc eeeeeeceeeeeeeeeceeeeeaeeeeeeeesaeeeeeeesseseeeeeessaaeeeeeeeeas 21 PC GUIMING IMAGES asii a ia aaraa a 25 Acguinng images USING INTA sisaan Ea 25 COMMUMMGNINDULS eee E a A E EE 26 Op mi ZNJ GISDA Y iesi a a AS 30 PACOIMA iagos irern E ec a a eaneesReaa iawn bells 34 Calibrating NOUIS sessin acess a A aaa a a EE 37 SAVING MAGS Srei E E E E T awele a 41 Showing scale Dal ernetan o a a ce the a e a aal 45 Saving Printing E mailing ccccsssceeesseeseenseeecenneesenseeeseenseesenseees 48 ye WAS ld te 6 eee ene ae ee eee eee eer a ee ee ee a a eee ees 48 PrnUnO IMAJO 5 ica ei errr is cease E Late beat ee ean ire ea 50 E MaMING IMAGES aeren aaa Meera teste stwrndiaiaaauth cigatinaiieniaghootaatatveuorel cutie 53 PAVOMIVINNG MAGES viris aa aa Ea ai EAE 57 Deine adatabaSe orraco a E G a 57 Define the director
216. n existing image object Keeping the left mouse button depressed move the mouse onto the image object within the report window When you release the left mouse button the image will be assigned to the report document You can insert a number of images simultaneously into a report Create a new report page that has at least one image object Select the desired images in the image da tabase or in the image manager and drag the selected images onto the first image object If the number of images selected is greater than the number of image objects repre sented on the current report page your image analysis program will automatically add any pages needed The added pages use the page template of the active page Please note that you cannot reload an image already inserted into a report into your image analysis program The sequence of the images inserted into the report is determined by the sequence in which you select them from an image database Mark the images in the order in which you want them to be inserted into a report To do this depress the Ctrl key and mark the images with the left mouse button The numbers in the top right corner of each thumbnail represent the order of the selection The images from the image manager are always inserted in the sequence of the im age buffers The order in which they were selected is of no significance You can insert all image types which can be loaded by your image analysis program into a report
217. n the same group with other parame ters of area Click on the Density group of parameters within the tree view e g to list density parameters only e You can also rearrange the order in which measurement parameters are listed Simply click on one of the two column headers to have parameters sorted alphabetically according to the header Particle parameters are measurement quantities which can be measured for each detected particle Image and text descriptions of all parameters are avail able within the dialog box To view a parameter s description in the lower part of the dialog box simply leftclick on it e g the measurement parameter called Area The sheet lists some particle parameters from a total of about 100 possible ones a aaee parameter ID Particle laa Diameter Outer Distance Max Shape Factor Unique ID number of the particle Area of the particle in the unit of the current image calibration The area is calculated by multiplying the number of pixels by the calibration factors of the X and Y axes The sum of the pixel distances along the closed boundary The maximum diameter through the particle center from outer border to outer border The maximum distance of parallel tangents at opposing particle bor ders A shape factor informs you how round a particle is A shape factor of 1 is a circular particle all other particles shape factors are less than 1 The calculated shape factor can also be great
218. nal ID e g Project in the upper Format field with any other text You can use the wildcards lt Date gt and lt Cons No gt 4 Click OK to close the dialog box 5 Set up a new database folder gt The new standard name will now be offered in the insertion mask Insert Images Background Information Insert Images There are several options for inserting images into a database folder e Menu commands mark the database folder in the tree structure of the data base window Select the Database gt Insert gt Images command e Context menu mark a folder in the tree structure of the database window and click on the right mouse button to open a context menu Select the Insert gt images command e Drag amp Drop in the image manager drag the images from the image buffer down onto the database symbol in the image manager The images will then be inserted into the active database folder e Drag amp Drop into the database drag one or more images from the image manager into a database folder When you do this you can see the images in an entry in the tree structure The images will then be inserted below this entry You can also see the images in a preview window or as thumbnails in the gallery view The mouse pointer will show you by way of its form whether or not the Drag amp Drop operation you want to perform is allowed The table below shows the mouse pointers you may encounter when you carry out a Drag amp Drop oper ation
219. napshots are optimized independently of one anoth er The optimization of the exposure time occurs continually and automatically Before you can use intX for the first time your image analysis program has to cali brate the camera This calibration is solely required to determine your camera s spe cial properties which are required for the automatic calculation of the exposure times To carry out this calibration simply follow the directions your image analysis program gives you intX uses the calibration data of the active input channel for the XY calibration of the images Intelligent Exposure oj o Options live Exp 100 0 ms Snap Esp 91 71 ms Ge Acquiring images Configuring inputs Step by step Step by s tep 26 Acquire images using intX This command is not available for all cameras and software configurations 1 Select the Images gt intelligent Exposure command gt The intelligent Exposure dialog box is opened When using this dialog box you still retain access to all of your image analysis program s other func tions 2 Should this be your first time using intX you will receive the message that your camera has not yet been calibrated Follow the directions 3 Click the Acquisition button to begin the live acquisition gt The exposure times calculated by intelligent Exposure are displayed in the dialog box s status bar The term Live Exp Live Exposure Time stands
220. nd ROIs J of particles p C tla Features Angle Dengi Dersi Dengi Dengi Densi Area IL iD 2 List of available measurements wi i E E p iem i 7 i TEE EF IOA voeca f 3 4 a a a 3 L c m 1 Tree control 3 cx amp 2 y EUD T24 uw gt eS S28 a 5 ose eeegs Js 8 FC ESS wi a aS Songar r wY H H iH H HOR uoa0aadad 153 AID ID Farticle HID iD Class 3 List of selected measurements Active Dnentation Measurement Filter settings The area of a parlicle is number of prels of the w o Ea x particle times calibration factors in X and Y direction M 23070 F ty X Particle parameter description e You can make the dialog box as big small as you wish press the left Dialog box properties mouse button while pulling an edge or corner of the dialog box in the direc tion desired 154 Image Analysis Detecting particles Background information Measurement parameter structure Particle parameter descriptions e The three areas within the dialog box 1 3 can also be altered in size What you can do for example is pull the separator between the tree view and the list of measurement parameters to the right while pressing the left mouse button giving you more space to view the tree view e All measurement parameters are arranged according to type in a tree view e g the Convex Area parameter is i
221. nfiguration versus Workspace e Defining GUI layout You may want to define workspaces for each of the various kinds of tasks thus optimizing how the graphical user interface is laid out for each of these Sepa rate workspaces could be for image acquisition report generation and image analysis Having separate workspaces gets you the onscreen layout you need and fast e Reloading images documents The path names of currently loaded images and documents can be saved ina workspace Saving the current GUI in a workspace at the end of your workday makes it totally easy for you to continue where you left off the next morning Any and all images sheets diagrams database s report s that were loaded when you saved the workspace will be right where you left them Be sure to save all your images before shutting down your image analysis program Any unsaved images will be deleted without prior warning The Special gt Configuration command enables you to individually determine ele ments on your user interface as well Please note that the configuration and work space contain different elements of the user interface Configuration refers to what commands have been defined for menus button bars and keyboard e g user de fined button bars A configuration saves what functions are available on your GUI A workspace however actually saves what the GUI looks like including specific doc uments The information saved in workspaces and configuration
222. ng the particle will turn red The pixels comprising the particle are those connected to the blue point of reference within the tolerance range set If e g the point of reference has a gray val ue of 75 and Tolerance is 50 then all gray values from 15 125 are within the tolerance range Image Analysis Classifying particles Background information 5 To alter the point of reference simply leftclick somewhere else within the image 6 To increase the tolerance range simply move the mouse to the right while pressing the left mouse button To reduce tolerance move the mouse to the left while pressing the left mouse button The status bar displays the current tolerance value 7 8 Rightclick to append the particle 9 Rightclick twice to return to the Append Particles dialog box Use the magic wand to add more particles 10 11 Feel free to select other methods of appending particles To successively delete appended particles one at a time simply click the Undo button You may only remove particles as long as the dialog box is open 12 Close the dialog box via OK to confirm the particles you have appended gt The manually added particles are now considered part of the current detection There is no distinction made between particles detected automatically and those you have appended when measurement re sults are issued 13 Select the Analysis gt Particle Results command to generate a new results sheet in
223. nge Fields e All commands in the Database gt Administration menu apart from the Logon command Make a note of your database password Delete records C No limit i Absolute C Percent Defining a session password 1 Select the Database gt Administration gt Change Session Password command 2 Enter a password in the Password field Remember which characters are upper lower case 3 Retype the password in the Confirm Password field 4 Confirm the session password by clicking OK 5 Select the Database gt Administration gt Logoff command gt The commands for changing the database structure are now gray Use the Database gt Administration gt Change Database Password command to protect your database with a password It can have up to 14 characters For security reasons you have to enter the password twice consecutively a special character appears for each character The command is only available when the database is opened exclusively Archiving Images Protect with a password Step by step 6 Select the Database gt Administration gt Logon command if you want to release disabled commands Assigning a password to the database 1 Open the database exclusively e Todo so mark the Exclusive check box in the Open Database dialog box 2 If the database is protected by a password select the Database gt Administra tion gt Logon command and enter the session password
224. nsfers the actual gray values onto the maximum gray value range Contrast is only increased if the image does not have any black pixels and any white pixels 5 Activate image buffer 1 Set image buffer 3 to be your destination image buffer Select the Oper gt Intensity gt Optimize Contrast command LOL 102 Processing images Increasing image contrast Step by step e This command extracts 3 of the darkest and brightest pixels from the his togram and makes them either black or white The remaining histogram is then spread to cover the maximum gray value range 6 Activate image buffer 1 Set image buffer 4 to be your destination image buffer Select the Oper gt Intensity gt Equalize Contrast command e This command assigns new gray values to the pixels of the image to have all gray values occur about equally frequently any gray value that occurs frequently will be spread out over more gray values This makes structures visible within image areas that have similar brightness The original image and the results of various contrast operations maximizing contrast means that existing gray values are transferred to cover the maximum gray value range Opti mizing contrast makes 3 of the darkest and brightest pixels either black or white and spreads the resulting histogram to cover the maximum gray value range Equalizing con trast means that exist ing gray values are spread out evenly to cover the entire gray valu
225. nt sheet showing the propor tional area of each phase in Each gray value phase is shown in a different color in the false color image Image Analysis Detecting particles Step by step fa Phase_Analysis Pale x Phase 1 0 51 Area Phase 2 52 137 Area Phase 4 209 255 Area 1059 21 1479 79 3078 78 4315 1517 20 399 66 596 78 1323 42 46 12 549 58 845 20 1239 55 2472 04 43 21 1164 29 775 94 1179 44 2592 94 45 32 1172 76 680 52 1099 23 2100 71 44 04 889 36 473 19 699 55 1645 41 50 61 433 28 441 52 645 05 1489 68 45 82 675 18 825 76 1315 63 2471 70 43 10 1121 89 494 86 729 95 1746 13 49 55 553 26 11 Select the Measure gt Phase Color Coding command to generate a false color image based on the gray value phases defined gt The false color image will be written into the destination image buffer gt The color of the phase will correspond to the header color in the mea surement sheet 12 Now load the next image you wish to analyze 13 Select the Measure gt Phase Analysis command gt The thresholds currently set are still valid Phase analysis will be con ducted based on these thresholds gt The measurement values will be appended to the existing sheet Detecting particles During an automatic particle analysis your image analysis program automati cally looks for particles on an image The color or gray value is the criteria for the recognition of a particle Therefore in order to ha
226. nt values Lol 128 Creating 3 D surfaces Creating 3 D surfaces Background information Creating 3 D surfaces Creating models Background information What are height images What are texture images 3 D surfaces via EFI images Calibrated height images Step by step Height map above left and texture image above right of a pitch specimen Confocal laser microscopes scanning probe microscopes and stereographs provide height maps of an object s surface the heights measured are encoded in a gray value image Height is in proportion to pixel intensity values using the above mentioned methods The height map is used to create a three dimen sional representation of the object s surface You can have the gray or color image of the object surface placed over the 3D model of the height map to serve as texture The color information will be com bined with the height information making the model look especially realistic The Extended Focal Imaging module enables you to compute an EFI image us ing a series of images of a surface at varying levels of focus All areas of this EFI image will be clearly focussed Furthermore you can also generate an EFI height map The height map has to be averaged using a smoothing filter e g using the Oper gt Filter gt NxN command The 3 D model of the surface is then generated using the height map Use the EFI image to texturize the 3 D model The calibrated height val
227. nto four sections in the standard full view button 1 Fhase analysis ExampleD atabaze apl H Eg Wafer H Eg Extended Acquisition H Eg ae Image lignin ee analysis H a TEM acquisition H Cg Stereo images H Eg Extended focal imagir H Eg Filtering H Ca Particle analysis Passe n H O Calibration images analysis Docu H CA Fluorescence Image f H Eg Cast iron H Eg Grain size analysis H Eg Micro hardness H Eg Paint on aluminum 3 Sel 1 0 kE A gy Button 1 remains fasaa TE v alal ileal elal fem gales ev alal ale dep ress a Datensatzname Yergroherung ed in full El Rough End 10000 view You can alternate alline Grating 8300 E Glomerulus 5000 a Cytoplasma 13000 al Crystal Struc 16000 E Brain 4000 al Adeno 160000 between gallery view left and table view Peet ais right by clicking the TEM Aufnahme TEM Aufnahme Next View button 3 Feldname Feldwert CQ Wafer Beispiel TEM Aufnahme a TEM Aufnahme Modul Aufnahme 3 Stereobilder Datensatzname TEM Aufnahme 3 Schichtdicke Datensatz Nr 28 Datum 08 11 2002 Zeit 14 38 E Beispieldatenbank apl S SSN SN BT SN y Beispieldatenbank apl E TEM Aufnahme 3 Stereobilder C Schichtdicke C3 Phasenanalyse RSN Q3 Partikelanalyse Line Erai R C3 Multiple Image Alig Ca Mikrohartemessune J Phasenanalyse
228. ntry or database field can be Three differently for am matted field objects il 1 Field name lustrate the variety with 3ieme ppe MRA An which field objects can appear in a report Field entry 3 i E a iEh Dop a ae a il AS j nF S 6 I I u Image height 4099 mm Qe Available field object components text variable placeholder for the The field name is dictated by the definition of the fields in the data name of the database base When you insert a field object the contents of this object will field be automatically replaced with the field name selected You can replace the field name by a definite text To do so dou bleclick the field object in the edit object mode The field name can be edited in the Record Fields tab text variable placeholder for the con The contents of the database field is different for each image and tents of the respective is automatically filled out anytime a record object is inserted into a database field i e the report from an image database The lt Calibration Unit gt field entry field entry will be replaced by e g mm if the image has been calibrated in This text variable ap mm pixel aus srl Fi aes You can format this text object just like any other Of especial note ets When the field ob is that you can permit multiline text thus allowing space for data ject is inserted the field base fields such as the Memo type name ap
229. nts command runes 2 Activate the Classes tab to determine the parameters you wish to include in the measurement sheet 3 Select the parameters desired e g ID Class and Particle Count To do this select the check box next to the parameter desired It will then appear in the Selected Measurements list gt The parameters selected will be moved to the Selected Measure ments list and will appear in the results sheet for each class e tis advisable to include the ID Class parameter in the results sheet to be able to see what results go with which classes e The lower part of the dialog box shows a text and graphic definition of any parameter you select 4 Click on OK to close the dialog box om f 5 Select the Analysis gt Class Results command Bat gt A sheet containing the results of the class measurement will be gen erated Image Analysis Classifying particles Step by step All particles which cannot be assigned to a class will be put in the 0 class and included in the sheet as well The carbon fibers are divid ed up into two gray value phases The classification offers a results sheet with the following classification parameters amount of parti cles mean gray value and mean area of the particles in a Classification 98 a 99 101 104 103 100 102 109 4 4410 14 19124446 110111 145 oe 119 122 1124 426 150 149 156 155 160 159 163 162 169 168 153 42 20 90 126 12 Filtering class
230. o base your new report template on 3 Select the Template option in the Create new group Only via this step can you decide that you want to create a report template and not a report 4 Confirm via OK to create the new report template gt You can always edit only one report or report template at a time This means that if you still have a report or report template that is open you ll be asked whether you d like to save any changes made or not gt The report currently open will be closed and the first page of the report tem plate will be loaded into the Report window gt The Graphical User Interface GUI for editing report templates is some what different than the one used for creating and editing reports You ll know that you are editing a report template and not a report because the background is gray Report Generator Creating saving new templates Step by step Adding a new page template for several images You wish to add a new template page that is to contain 6 images r 1 Click the Select Page Template button in the report window button bar to open a list of all template pages defined in the current report template 2 Select a page template you can base your new page on and confirm via OK Try to use a template page as the basis for a new page layout which already contains all of the important standard elements of a report page gt The report window will now display the template page selected 3 Click the
231. o limit the search to images Other documents will not be found 4 Click the Search button to carry out the search gt The images found will be displayed in a separate database folder with the name Query results The query results are displayed directly under the database icon in the tree structure gt Some information about the current query is displayed in the form for example the number of records that have been found gt The current marking jumps into the query results automatically G8 86 Archiving Images Work in the database window Background Information The Query results database folder shows all the data that has been found The form contains information about the query Load data Query results eu ITEM apl a EN Query results Query type Query by example E C3 Materials science SQL command select from Images where RE H CA BioMedical science Matching records 45 H General ITEM Query results Set 1 OkB 2 5 Use the Previous record in history button to return to the record which was marked before the query was carried out 6 Mark the Query results database folder in the tree structure 7 Mark one of the images that has been found Click the right mouse button and select the Goto Record command from the context menu gt The marking in the tree structure jumps to the database folder which contains the selected record 8 Mark the Query results database folde
232. o the right or left backwards for wards 6 Rightclick to terminate definition of the length to be measured e Define more lengths within the model as desired The colors used for displaying points and lines are cyclically varied Corresponding measurements in the measurement sheet are the same color 7 After you have finished measuring simply rightclick Click on Yes to con firm Three distances measured within the pyramid shaped indentation ERE ERE EE 129 03 156 19 134 36 How do I accumulate measurement results 1 Length measurements of different models can be written in one measure ment sheet First load or generate another model Then activate the mea surement sheet and select the measurement command gt The measurements you make now will be appended to the active measurement sheet Current measurement results are the only ones shown in the 3D window ZEL 138 Creating 3 D surfaces Measuring models Step by step Saving showing hiding measurement results 1 Measurement results are not saved with the model They will be deleted when you close the model To save the measurement results you have to save the measurement sheet containing them e Use the Measure gt 3D Measurements gt Hide Measurement Results command to make measurement results disappear from view in the 3D window e Measurement results currently hidden can be re shown at any time within the model being measured Simply
233. ocuments into a database folder then you must arrange the organizational fields explicitly for the insertion mask 2 Extend the display of Form View To do this doubleclick for example on the Form View entry or click on the plus character in front of it Archiving Images Arrange Fields Step by step e You can adopt different database fields into the form view for the lt Folder names gt Image Graph Document and Data data types The lt Folder name gt is different for each database and reflects the organi zational ID of your database 3 Mark the database folder In a project database the database folder is called for example Project gt The Available and Current list display all organizational fields which relate to all the information within the database folder The required fields are formatted in bold type 4 Mark the Customer entry in the Available list and click the Add gt gt button 5 Doubleclick on the Form View entry in the View Type list to display the data types for the form view 6 Mark the Form View gt Image data type gt The Available and Current lists now contain all existing database fields 7 Mark the Customer entry in the Available list and click the Add gt gt button 8 Repeat the last two steps for all types of data gt The customer will now always be displayed in the form view 9 Now mark the Insert view and the Image data type 10 Transfer if required the Customer organiz
234. of the report generator is in the button bars The Re port and Report Objects button bars are the two most important button bars Report button bar Turning button bars on and off Report Generator Creating reports Background information Report Window Report Report Objects Button Bar Button Bar Mi a Graph 3D C Modue Special Winds f ie Arah m re Fa a p P B kimini Di L Kalas PPI AIO Phas H3 Liver Tissue EFI Crystal EFI_MAP Cry 22 08 20 04 Pyramid Page 1 1 Foston 000 mm Size AUU E Learils 30 Sulace S Heni h Read Tm Coloris II D4 fe The report button bar is a part of the report window Please keep in mind that these buttons functions are not available as menu functions This is why this button bar should remain visible If you like you can use the Special gt Edit Button Bars com mand to show or hide the button bar or to add other frequently used buttons e Use the Special gt Edit Button Bars command e Rightclick in a report window All button bars linked to report generator are listed beneath the Button Bars command 691 170 Report Generator Creating reports Background information H Paging through a report Go to Hl Add Page Delete Page Report properties File Format F 4 First Page Previous Page Next Page Last Page Add Page Delete Page set Zoom Cy SIS eles poo ole ill re
235. of thresholds two particles for example touch one particle detection another at the marked section and are detected as one single particle figure 1 The Analysis gt Delete Particles command eliminates the wrongly detected par ticle figure 2 Use the Analysis gt Append Particles command to add particles separately The magic wand function is for setting thresholds for each of the two particles sepa rately figure 3 Particles 100 and 101 will now be recognized as the separate particles they are Because of their different shape they will be classified in different classes and thus appear in different colors figure 4 Ba Pa m o t 2 6 e 4 a a ees vege eee ee RRK ar uk re Eo E a oe EEA es aur Warning Please note that conducting another detection following interactive editing will overwrite the particles you added interactively thus yielding the same results you had before editing Therefore the Analysis gt Detect command should not be used again after editing a particle analysis interactively You may however generate a results sheet for your measurement results and or select new mea surement parameters as these do not require further detection Warning Please note all the particle filters you have set also apply when you append par gt ticles interactively image thus enabling you to define particles that would not otherwise be includ ed in thresholds set for the whole image All you do is se
236. oil painting makes an image look like a poster Mosaic adds a mosaic like pattern to an image s appearance as shows objects in relief Dark objects appear raised light ones as depres sions Noisify adds random pixels to an images i e noise Noise values can be added for all color channels red green blue or just for one Histoequal linearizes the number of pixels per intensity value This accentuates details ize in dark image areas Stretch In increases image contrast tensity inverts pixel color values The resulting image thus looks like a photo nega tive Step by step Using multiple RGB Studio filters You wish to improve the appearance of an image To do so you want to conduct gamma correction increasing image sharpness and improving image contrast 1 Activate the image buffer with the original image e Simply leftclick on the image buffer that has the original image in it 2 Set the destination image buffer gt Your image analysis program will propose a destination image buffer To alter the proposed destination image buffer drag the desired image buffer while pressing the left mouse button from the image manager onto the operands box 3 Select the Oper gt RGB Studio gt Apply Filters command gt The image window will be minimized A separate preview window showing the image in the active image buffer will appear gt The Apply Filters dialog box will be opened 4 Select t
237. om the tree structure onto the image buffer e Please note using these two methods will load the image but not the i documents which may be attached to them Loading several images in a defined order 1 If the images that you want to load are in different database folders carry out a query to find all the required images Search for example for all the images which have been inserted for the projects A and B gt All images found will be displayed in the gallery view 2 Mark the images in the order in which you want to load them To do this depress the Ctrl key and mark the images with the left mouse button gt All the marked images have a colored background The numbers in the top right corner of the images represent the order of the marking 3 Mark an empty image buffer in the image buffer box 4 Select the Database gt Load Document command gt The marked images will be loaded into the successive image buffers of the image buffer box in the selected order If one of the image buffers is write protected your image analysis program stops loading at this point gt e Please Note images in image buffers that are not write protected will be overwritten without warning Z8 88 Archiving Images Work in the database window Step by step If you mark several records the records in the gallery are numbered on the top right in the order of selection Select the Load Document command to load all the selected i
238. ommand Global settings Select the Special gt Preferences command to adjust a broad range of pro gram properties The following settings are relevant for particle analysis e Measurement sheets to alter font font size number of decimal places for measurement sheets go to the Sheet group of the View tab e Overlay to set font size for particle parameters in the overlay go to the Overlay group of the View tab Enter the number of decimal places particle parameters are to have in the overlay in the Measure tab Step by step Selecting measurement parameters Tp 1 Select the Analysis gt Detect command to execute detection i e You do not need to select the Detect menu command if you have al ready executed detection via the Define Detection dialog box He 2 Select the Analysis gt Define Measurements command 3 Activate the Particles tab to determine the particle parameters you wish to include in the measurement sheet 4 Click on the top directory called All in the tree view on the left side of the dialog box to view all parameters listed alphabetically in the Measurements list 5 Select the parameters desired to do this select the check box next to the parameter desired It will then appear in the Selected Measurements list All the parameters listed here will be included in the measurement sheet GGL 156 Image Analysis Detecting particles Step by step subsequently Select the check boxes for Phase A
239. one or more objects and use one of the buttons of the Position button bar to move the object selected in the direction desired Each click represents 0 1 mm e Select one or more objects and use the Position and Size tab if you wish to enter the position of an object as an absolute numeric value When you select an object its exact size and position will be shown in the status bar When positioning or altering the size of objects its dimensions and current position are shown in relation to the rulers of the report window You can turn rulers on or off in the Report Properties dialog box The unit of the rulers is also determined along with the report properties The following units are available cm inch mm and pt Use the grid as a positioning aid while inserting objects You can display the grid in the report properties and alter its size When inserting an object it is automatically aligned on the grid Use the buttons on the Align button bar to arrange numerous objects relatively to one another The position of the reference object is crucial for alignment The reference object is the object you last selected It s easy to recognize with its gray selection markers any other objects have white selection markers Position and size of the reference object is unaffected by operations conducted Alion OOOO lt m g l e ss g wt tek G24 176 Report Generator Report objects Step by step Mirroring You can mirror an
240. or all other image formats e f possible compress the images to keep the size of the e mail to a mini mum Use the JPEG image format if the recipient wants to open the imag es with another application program since most application programs can not load compressed TIF images 7 To determine the file format for sending reports select the Report tab located in the Send email Preferences dialog box Select the Send report in Rich Text For mat rtf option if the recipient wants to open the report in another application program such as MS Word For RTF format you can reduce the resolution of the images in the report 8 Close the Send email Preferences dialog box by clicking on OK 9 Please Note Select the Custom option in the Send email dialog box to activate lt P the format settings your have just made 10 Click the Send button gt Allimage and document files selected will appear as attachments in a new e mail document e Please keep in mind that as long as the e mail document is open all other functions in your image analysis program are not accessible GS 56 Saving Printing E mailing E mailing images Step by step All selected documents will appear in the e mail as attachments Untitled ware as a B Diagrm1 sfd SKB Sheetl sqd 6KB Text1 txt 3KB R sfs SKB M txt 3KB txt SKB z apan tif 260KB Archiving Images Archiving Images Term definition Archiving Images
241. ormat tif is advisable generally e The File gt Arrange Image File Formats command is for putting image for mats into the order you wish i e most frequently used formats at the top of the list image formats you don t need can be disabled 5 Click the Options button in the Save Image As dialog box to access general settings related to saving images gt The Save Image Options dialog box is opened together with the TIFF tab 6 Select one of the compression methods offered from the Compression list Se lect the None entry to save the image uncompressed e Please note When an image is compressed this generally results in arti facts Therefore you should only compress images that you have finished analyzing or measuring 7 Define how image overlays are to be treated e Clear the Burn overlay into image check box The image overlay will thus be saved along with the image but will remain a separate object in the im age file This means that the image and the overlay can still be displayed separately and also be edited when you load the image file No image in formation is lost in the process e Select the Burn overlay into image check box when you re planning on ex porting the image to another application e g MS Word This is the only way that overlay information can be read by another application 61 50 Saving Printing E mailing Printing images Background Information 8 To confirm these settings click on
242. ort template will have to be adjusted so that it fits your own database eon nna ce Templatel Page Template PageT emplatel have toinsertanex S m lelte Eye isting record object first You can do this on any page you please DataB aseO bjectWithS hadedFields BObjectWithN ameAnd mageWidt C To alter a record ob ject select it left click Then switch over to the edit ob ject mode by clicking on the e Edit Object Template button You can select the field ob jects individually in the edit object mode and then delete 1 1 them as needed Position 5 0 10 0 mm Size 160 0 80 0 mm Z Use the Field button w Templatel Page Template PageTemplate1 lol x in the button bar of the report window to miey pa jes lee Veet eee 75 E jl Gl jeden edie Bilt insert new database field objects You can select any of the database fields defined in the active image database Report 0b Select Field O Parent ID O Path Record Name O Record Version O RecordT ype O Remote Database ID O Remote Record ID SSL 186 Report Generator Report objects Step by step To save an adjusted Templatel Page Template PageTemplate1 El record object in the LE O o report template simply close the edit object mode by clicking on the Finish Object Editing button Channel lt Channel gt Manual lt Manual gt m a oO T 7 Position 0 0 0 0
243. orts and the maximum amount of viewports You can enter a comment for each image which is then saved together with the image Use the display properties to show this image comment in the viewport The Display Properties gt Visualization tab enables you to select a false color view for all loaded gray value images This button enables you to increase or decrease the size of the image in the active viewport by increments of 100 Display Co First Steps Displaying multiple images Step by step nfigu This button enables you to save all viewport settings You can also link images with ration viewport settings which can be loaded together with the viewport settings Select Viewport You see a schematic monitor in the viewport manager This button enables you to de Manager Pane termine what is to be shown in this monitor Three views are possible Select one of the 3 pos sible views from the viewport manager Dual Screen System Step by step The viewport view is the default view It shows you the current order of the viewports in the image window In other words you see the image window in a schematic view The image names and numbers of the image buffers are shown in the image buffer instead of the images You will need this view when working with dual screen systems The navigator view shows the image in the active image buffer The image is com pletely shown in the navigator You can define the image section which is s
244. ouble arrowhead While pressing the left mouse button you can reduce the frame in size The length width ratio of the frame will be the same as the viewport in the image window e Now move the mouse to within the red frame The mouse pointer will now turn into a four pronged arrowhead You can move the frame by moving the mouse while pressing the left mouse button gt The image segment you selected will be shown in the image window 11 Magnify the images zoom factor so that only one image section is shown in the image window Use the slide control located in the image window to move the image section gt The frame in the navigator moves accordingly and once again shows the current image position Within the thumbnail in the viewport manager you can define which HARA e A BIS image segment is to be mjm aa displayed within the im age window To define the segment adjust the size of the frame and move it to where you want it within the Navi gator Yiewport M anager Ei Saving GUI configuration Background information Workspace You can save your graphical user interface in a file This is called a workspace A workspace includes the layout of all document windows and button bars as well as how viewport and image manager are positioned It can also include specific images and documents you wish to have loaded Le 22 First Steps Saving GUI configuration Background information Warning Co
245. ould always try to insert graphs as records because only then can you define database fields and thumbnail is available in the gallery view You can insert a data record into a database folder which is not linked to a document You can use this possibility for example to improve on the structure of the data within a database folder e g several investigation methods have been used for an order but they must all be described by their own record Under each investigation method you can now insert the investigation results images or sheets Arranging data base fields Arrange the organizational field Customer so that the customer is displayed in the form view for all types of data When an image is inserted the customer should be displayed as information in the insertion mask 1 Select the Database gt View gt Arrange Fields command gt You will find in the View Type list in the Arrange Fields dialog box all the contexts in which database fields can be displayed e Remember that user defined database fields are not automatically visible in every view but must be explicitly arranged One exception is the inser tion mask User defined database fields are adopted automatically into the insertion mask Remember that organizational fields only appear automatically in the insertion mask when a new database folder is created If the information from the organizational fields is also to be displayed when inserting images graphs and d
246. our image analysis program suggests the selected descriptive term with an additional No as the folder name The folder name defined here reap pears later as identifying term in the insertion mask 7 Click the Next gt button 8 Click the Next gt button without defining your own database fields 9 Click the Finish button How to set up an express database Archiving Images Set up a new database Step by step The new database is called ExpressDatabase01 The database files and all of the saved files that are to be added to the database are saved in this directory Database ExpressD atabaset Database files api co NAarchiveE xoressD atabasel Browse Hew Database How would you like to organize your database ie Express The Wizard generates a predefined database ou may shore your documents in the Folder 1 folder as well as create your own folders for storing documents Hew Database i Select Finish to let the database assistant create a database with the following settings Cu i Name ExpressD atabasel Location of database files cW4rchivesE xpressD atabasel Location of images and documents c V4rchiveExpressD atabasel Organized by Folder Organizational ID Folder name Save settings as new template Check your database s settings Back Cancel amp ExpressD atabaseO1_apl sl i Fa Elle yglan 4
247. p by step The above figure shows a list of all types of doc 7 uments that canbee Y ee mailed via your image a Diagram 515 Diagram std analysis program as Graph 1 analyS S Graph sqd well as their respective e Image 1 Tagged Image Format tif standard formats Report Rich Test Format rtf w FRA Sheet 515 Sheet sfs MER Text Test bet w e Text Text txt Document 3 To clear all selections simply click the Unselect All button Select the docu ments you re interested in by clicking on the corresponding check box in the document list e A warning message will appear if your attachment exceeds a maximum size 4 Select the Add attached database documents check box to send a record and any appended documents images sheets graphs etc e An entire image database cannot be sent via e mail 5 Click the Preferences button to set file formats for all images sheets dia grams and graphs gt The Send email Preferences dialog box will be opened 6 Select the Image tab in the Send email Preferences dialog box to define the im age file format File formats are always defined for all the respective documents of one single type not for one single document e The TIF format is default Select the Burn overlay into image and Convert 16 bit images to 8 bit check boxes for this file format if the recipient will open the images with another application program This will be automati cally done f
248. pears here E layout function such as frames and rectangles for use as colored highlighting for text object image ob layout function e g An image object defined in a field object cannot be used later on ject pictograms represent as a placeholder for images You cannot insert a new image into ing the various data this image object in this report base fields To save space be sure that you always insert images as links If you don t images will be re copied each time you insert a field ob ject into a report field object The template for a field object may include a field object which must however refer to a particular database field e g Calibration unit You can then insert several database fields e g Height and Width which will then always include the record object s unit of calibration 6 text standard text to be printed with every database field Report Generator Record objects Background information Adapting record objects If you are using a database that does not have some of the fields that the record ob ject does then when you insert this kind of a record these field objects will simply be ignored You will not get an error message and the entry in the field object will remain unaffected This deals with placeholders for sheets diagrams or diagrams The placeholder re mains empty if no sheet diagram or graph is attached If you wish to use record objects the record objects in the rep
249. play data check box to have length width and height shown 5 Close the Modify 3D Surface dialog box Setting resolution 1 Click the Modify 3D Surface button Surface button bar at the lower edge of the 3D window 2 The entry you make into the Step width field determines whether e g ev ery 10th pixel of the height map is to be used for the display of the model if you enter 10 e The default entry is 10 In many cases this is in fact a suitable com promise 3 Increase the step width if the model has too many peaks obscuring the model s primary structure thus interfering with the overall visual impres LEL 132 Creating 3 D surfaces Editing models Step by step sion the model makes Apply a smoothing filter e g Oper gt Filter gt NxN to the height map be fore creating the model to reduce high contrast transitions and to avoid sharp edges D Decrease the step width if the model appears unnaturally rough or if signif icant surface detail is not apparent The lower the step width the slower the motion of the model because more points have to be computed for display of the model 5 Select the Display as grid check box gt The continuous model surface will disappear from view and be re placed by a grid representing the surface structure The height of the grid nodes are computed via the corresponding intensity values of the height map Any interjacent height values of the model will be co
250. program supports a broad range of compression methods for reducing the file size of images you re saving This is important when e g you wish to e mail images The JPEG compression method provides excellent results for gray and true color im ages JPEG does however cause image artifacts the higher the degree of com pression the more the artifacts JPEG compression reduces file size considerably 4 097 kB JPEG quality 75 504 kB JPEG quality 50 327 kB JPEG quality 25 219 kB Saving Printing E mailing Saving images Step by step Uncompressed image at 50 zoom upper left and 400 lower left JPEG compressed im age quality 5 at 50 zoom upper right and 400 lower right High magnification low er right clearly shows the artifacts resulting from extreme JPEG compression Step by step Saving images 1 Activate the image buffer containing the image you wish to save 2 Select the File gt Save command e You can also save the image by simply dragging amp dropping it onto the save icon in the image manager gt The Save Image As dialog box will be opened 3 Enter the path of where you wish to save the image Enter a name you wish to save the image as into the File name field Your image analysis program will automatically propose the image s current name to be used as the file name 4 Select the desired image format from the Files of type list The TIF format Tagged Image F
251. r again Use the Del key to delete the search result Background Information Load stored data Integrate images in reports Export images If you have already archived part of your data on removable data media the system searches for a data medium with a fixed name when loading This explicit data medium name is automatically assigned by the system during filing You will be asked to label the data medium with the name To load the data insert the required data medium Then select the DocumentFiles directory or click the Query button Use the report generator to produce professional multiple page reports File gt Report gt New It offers layout options for the highest standard of reports Images docu ments and database fields can be easily integrated directly You can also import values from previously specified table boxes into a report You can copy database images and documents as files onto any network drive at any time Database gt Export record files You can then edit these files using other programs and also print them out Archiving Images Load data Step by step Step by step Loading an image 1 Mark an empty image buffer in the image buffer box 2 In the database document s gallery view doubleclick the image you want to load gt The image is loaded into the image buffer and represented in the image window e Alternatively you can drag amp drop the image either from the gallery view or fr
252. r images resulting from an image operation and which are based on the original image LOL 162 Image Analysis Detecting particles Background information Class parameters Class parameters are statistical quantities referring to all particles of a class The sheet lists some classification parameters from a total of about 100 possible ones eter Particle Count Features the number of particles in a particular class Area Ratio Area area percentage of all particles of a class rela tive to the search area frame or ROI 2 oO the sum of the areas of all the particles of a class the mean area of all particles of a class Particle Density Density the number of particles of a class per area rela sa tive to the ROI area Maximum Mini l upper lower class limit of a classification can mum Class be used to include a classification scheme in your results sheet Particle display Special gt Preferences Editing overlay display Define Detection gt Results To alter particle display go to the Define Detection gt Classification dialog box If you have selected No classification as your classification criteria then particle data will be shown without being classified Global settings for overlay display of interactive measurements are not relevant to automatic particle detection There are however exceptions e Decimal places fractional digits enter the number of decimal places for particle measurements sho
253. r its name in the General tab This tab is located in the text object properties The name of a text vari able has to start with the symbol Anytime you alter the contents of a text variable your image analysis program will automatically update all other text variables in the report of the same name You can change the contents of a text variable as often as you like in order to e g correct spelling errors Text variables are usually defined in a report template so you can structure headers and footers This means you only have to enter a heading that is to appear on every report page once You can define as many text variables as you like in your report templates e g for headings author project title department You can however also define text variables on a report page within a report When you change the contents of a text variable within a report this changes the contents of all the report pages containing this text variable It does not matter wheth er the report pages are based on the same or different page templates A text vari able can also appear on the same page more than once Text variables are only linked as far as content is concerned and not with regard to the formatting This means that just because you alter the formatting of a text variable does not automatically mean that the other text variables of the same type will be up dated in the report of lt Record Names 26 04 00 Repo
254. ration line between two particles is only one pixel in width then select the Adjacent borders 4 option Otherwise the separated particles will be considered one particle when detected 9 Click the Execute button to conduct particle detection gt All particles detected will be shown in the image overlay in color De termine how particles are shown in the Classification tab gt The most recently defined classification will be applied 10 Click on OK to close the dialog box Image Analysis Measuring Particles Background information a Detected particles appear in Bo iy ie 2 i aan eis ee ibe color in the image overlay The most recently defined classification will be applied to the image Any particles that cannot be classified will i S To Sai i le tif ty D Ho g ae i li tippy tity n cig City a eg iy ltt eat tty AP y r f Er Pd eee igi gt ty Cr P Z Yan itis iad Cag le o Lien es ee 124 Gog J ELA Ga Abd Oe Veer CGP 242 o NPT appear crosshatched ee A Opp A z De Cie lle lll Cll tite Welle le iy itp ape GY g ae iy lle ip funia A ty 0 Op CG G0 2Gn ee i PEL ie a J 2 p he ET D a Do tp Measuring Particles Background information The Define Measurements dialog box has three tabs for defining measurements classes a
255. re stored diagram or diagram or a graph below an image in a database can automatically graph be inserted into a report To do so create record objects with placeholders i e for a sheet Field objects Field objects are fields of text linked to the content of a specific database field They refer to a particular image database which must be open when creating a report Field objects are usually comprised of the name of the database field the field name and of the field entry itself They can however also include all other kinds of report objects excepting placeholders Field objects can only be inserted within a record object esl 184 Report Generator Report objects Background information Edit field objects You can only begin to edit field objects once you have clicked on the Edit Object Template button in the edit object mode moving you down a level within the edit object mode What make up field Field objects can in essence include all kinds of report objects Normally field ob objects jects contain at least the name and content of the database field Your image analysis program does not automatically adjust the length of the text ob ject to fit the field entries or database fields When a field entry is longer than the text object the field entry will be cut off on the right hand side You should thus keep an eye on how long your text objects are Decide their length depending on how long the longest field e
256. rea and Orientation for example gt The parameters selected will appear in the Selected Measurements list as well as for each particle in the results sheet The ID Particle and ID Class parameters must be included in the re sults sheet to ensure that particles and particle parameters are clearly correlated in the image overlay 6 Click on OK to confirm selection of measurement parameters EH 7 Select the Analysis gt Particle Results command gt A sheet which contains all of the detected particles of the selected measurement parameters is created The parameters are in the same order in the sheet as in the Define Measurements dialog box gt The measurements are exported in color in accordance to the current classification All measurement values which belong to a class are exported in the color of that respective class To deactivate the coloring clear the Analysis gt Define Detection gt Results gt Use colors in sheets check box Defining particle filters The particles of the original Original Oe Hole Count Count image differ in orientation average gray value and number of holes During particle detection these gt particles can be excluded using these very parame lt lt gt aa a cm ters All particles located and analyzed via detection are shown crosshatched In the upper right image only the particles with one hole have been detected In the lower left image only ae
257. results 1 Click the Define Measurements button in the Analysis button bar 2 Activate the Classes tab in the Define Measurements dialog box 3 Select ID Class in the Selected Measurements list Enter 1 into the Min field of the Filter Range group 4 Click on OK to close the Define Measurements dialog box sen 5 Click the Class Results button in the Analysis button bar to have the results Eile shown in a new sheet minus the class 0 results Altering how measurement results are displayed 1 Select the Analysis gt Classify command to alter how detected particles are displayed 2 Select Outline in the Particle outline group to have only the outline of the particles shown in the color of that class instead of particles having a solid color filling Crosshatched particles will have a white outline 3 Define the kind of particle labels desired in the Measurement label group select e g ID Particles to display particles numbers in the overlay Select None to cancel measurement labels G9 166 Image Analysis Detecting particles Step by step Detected particles can be displayed in the overlay in various ways left the parti cle appears in solid color The value is the particle ID The contour of the particle is shown to the right together with the area value To alter how particles are shown go to the Define Detection gt Classification dialog box 4 Click the Execute button to have the al
258. ring e g a value of 3 will exclude noise particles 4 Clear the Use ranges check box to detect all particles occurring within the thresholds set Warning Please note if the Use ranges check box has been selected the particle filters lt P gt which were set for the previous analysis will be applied to the current analysis e The Total count field shows the number of particles which were de tected during the previously conducted detection 5 If particles have inclusions which are to be taken into account when calcu lating particle parameters clear the Fill holes check box This is necessary for particle holes to be recognized as such e The Fill holes option affects e g how particle area is calculated The area of the holes will be added to particle area if holes are not recog nized e The Hole Count and Hole Area particle parameters Define Measure ments dialog box refer to these holes in the particles It only makes sense to use these parameters if the Fill holes check box has been disabled 6 Determine the image area to be used for detection in the Search area group Select the Frame option to detect within a rectangular image area If a frame has not been set detection will be conducted on the entire image 7 Define how particles which are not located entirely within the search area are to be treated in the Border particles group 8 Define inter particle connectivity in the Connectivity group e If the sepa
259. rocessing steps field ScaleBarToOverlay Image Information S Image information includes all information saved along with the image In the example shown the image name and the file name are not the same Any information you wish to have archived along with the image may be entered in the field for comments The absolute width and height of the image result from the calibration of the input channel Click the button with the speaker symbol to show the Audio button bar Use the functions in the button bar to record a spoken comment about the image Acquiring images Saving images Background information A large amount of additional data will be automatically acquired together with the images All additional data are accessible in the Image Information dialog box You can for example open the image information by double clicking on the image buffer Depending on the acquisition method the dialog box can contain different types of tabs Each image you load into your image analysis program will at least contain the Gen eral tab with the image names and the general image data Here you can also write comments about the image You can also acquire audio commentaries should you have access to the necessary hardware When you acquire images with your image analysis program you will also find the Camera tab with the most important camera settings For certain microscopes you can also automatically acquire data abo
260. rt gt The mouse cursor will change shape and appear as a cross shaped symbol 3 Now define a rectangular area where you plan on inserting the text The text has to appear within the area you have defined to be displayed and printed out gt The new text object has now been selected and the word Text will appear within it 4 Click the Properties button in the Report Objects button bar to format the text within the text object 5 Select the font and font size in the Font tab Select the Italic format for the text You can also decide on what color you want the text to be 6 Click the Apply button to try out the text formats selected in the report 7 Decide on what kind of text to use in the Text tab e Select the Multiple Lines check box if the image comment is to have more than one line The Word Break check box will now become available L6L 192 Report Generator Report objects Background information Inserting sheets e Select the Word Break check box so that your image analysis program cal culates wordwrap automatically This is the only way you can be sure the text will automatically adjust to any changes you make to the size and po sition of the text object e Clear the Word Break check box if you e g want to list single words one beneath the other Now if you need wordwrap you ll have to explicitly set the wordwrap within the text object via the Enter key Text format is now unrelated to the
261. rt Generator Text objects Step by step The report above contains various kinds of text These are described in the sheet below Texts that are text variables appear in square brackets Editable text objects have dotted lines within them as they are to be filled out with text Field objects that are automatically filled out when you insert a record object are put in square bracket i Lype c En Particular properties Insertion fig bo Object Properties dia 7 Report button bar fg box The Background Object check box in report caine only text Select and Move tab has been se ee avr variable The text object s name in the General Tot vare starts with an symbol qe On the General tab the text object re ceives the type AutoText The Report Object Properties dialog box now includes an additional tab Au toText IES text The Background Object check box NOT in a record or field HE bject Select and Move tab has not been object a Field object On the General tab the text object re only available in edit ob ceives the type AutoText ject mode Step by step Inserting text objects 1 Enlarge the display of a report page so that the text is legible Select an appropriate zoom factor from the Set Zoom list in the button bar of the report window e g 100 or enter the de sired zoom factor directly 2 Click the Text button in the Report Objects button bar to insert a new text object into the repo
262. rticles are correlated with their forms the lighter particles have a gray value of about 153 the darker ones around 130 2 Select the Image gt Set Thresholds command e When analyzing true color images the Set Color Thresholds dialog box will be opened The two dialog boxes for either true color or gray value images differ considerably from one another Br Thresholds Ea Manual Auto Settings Phase Particle dark Lowy 108 Color High HE Current Background Ell Delete Include Piel File Transparent Auto Diagram ia Smoath a al al Histogram WIE PEE OF Cancel Help 3 Select the Manual tab e The bar below the diagram shows you how many gray value ranges and or phases are defined Each phase has its own color 4 Delete all phases already defined except one e Todo this select an entry from the Phase list and click the Delete but ton As soon as only one phase is defined the Delete button will be come inactive 5 Select the Histogram entry from the Diagram group gt The diagram now shows the gray value distribution within the image frame you have set e The current threshold values are shown in the diagram as two per pendicular lines The lower threshold is blue and the upper is red 6 Mark the Current option in the Preview group gt The active phase is shown in color within the image so that you can view what affect your settin
263. s This function stretches the existing gray values to cover the maximum gray value range 0 255 Adjusting image color Processing images Adjusting image color Background Information gt The resulting image is written into the destination image buffer Modify Gray Values transfer function Brightness gt 5O 0 Contrast 50 0 Background Information RGB stands for red green blue HSI The HSI color space can be shown mathe matically by a double clicking The central ax is is the intensity the distance from the axis is the saturation and the angle corresponds to the hue The color wheel is a two dimensional projection of the HSI color space The color changes with the angle The satura tion increases towards the outer limits Function Max Stretch Change Save Cancel Help dd The RGB model is a model used for describing colors generated additively as is the case on a monitor screen RGB images are also referred to as true color image and can contain up to 16 777 216 256 x 256 x 256 different colors via the additive mix ing of the three primary colors red green and blue If all color components are at ze ro the image will be black mixing 100 of the three primary color produces white HSI is another model for describing color values HSI is an abbreviation for Hue Sat uration and Intensity HSI values of a color originate from RGB values v
264. s have to be separated so that each will be treated separately and not several as one Your image analysis program provides several possibilities here e Oper gt Morphological Filter gt Separate Particles The morphological filter is for generating separation lines The filter can be used on a binary image with white particles on a black background Any holes within particles will cause artifacts e Oper gt Filter gt Separator The separator is applied to the image directly It outlines particles or areas that have the same gray or color value The resulting image can be edited interactively after particle separation has taken place You can also trace the lines visually using this filter e Combining multiple filters The original image of a typical particle separation is a binary image of white particles on a black background Use the erosion filter to remove particle boundaries until all particles have been separated Then have a skeletal framework of the image background calculated for offset correction A log ical AND operation between the resulting skeletal framework image and the original image will result in boundary lines being drawn between the particles When working with true color images it is easier to carry out a particle analysis on the gray value images of some images In this case as a preparation for the particle analysis use the Oper gt Color Separation gt Intensity command to cre ate a gray value image from the tr
265. s in the Overlay button bar Processing images Editing overlay Step by step Step by step Inserting and formatting texts 1 Click the Overlay Button Bar button in the standard button bar to open the button bar containing the overlay functions gt The Overlay Button Bar button will appear pressed as long as the overlay button bar is being displayed 2 Click the Text button to insert a text object gt A rectangle will appear in the overlay 3 Use the mouse to determine the size and position of the text object Rightclick to have the text object transferred to the overlay gt The Object Properties dialog box will open 4 Enter your own text in place of the lt New text gt default entry in the Text tab e Text within an overlay object can be altered at any time via the Object Properties button 5 Select the Autosize bound check box to have text object size adjusted to fit the length of your text 6 Select the Zoom with image check box This makes sure the text size is always adjusted to whatever zoom level the image is at onscreen 7 Determine font font size style and color in the Font tab 8 Define the background and text frame color in the Colors and Lines tab 9 Click on the OK button to close the dialog box gt The text in the overlay will be altered accordingly The width of the text ob ject will be adjusted to fit the size of the text The selection markers are gray When gray this indicates tha
266. s inserted on 31 5 05 before 18 30 Document Insertion Time lt 18 30 all images which were not acquired using the Channel lt gt SlowScan SlowScan logical input channel all images with a magnification of 200 or Magnification gt 200 more all sheets ile name You can use this query for a search using several search criteria which you want to connect in a complex way using AND or OR links Search targets are Field C with C with all RGB and gray value ImageType RGB J eee ge ImageType Mono A a all image names which image name begin with A all images were inserted on Document Inser 20 5 2003 the 20 5 2003 between 15 00 tion Date eS and 20 00 Document Inser gt 15 00 lt 20 00 tion Time This query uses the standard SQL database administration language to formulate the search criteria You can use this button to carry out an initial query by example For subsequent queries you open the dialog box of the pervious query For queries by free filter and queries with SQL you have the possibility of saving your search filter so that it may be reloaded later if required e The data found is indicated in the Query results database folder directly under the database symbol in the tree structure e The Query results database folder is updated with the new query results for each search e Query results are no longer present after a new start of the pro
267. s is totally different The program interface can greatly differ in appearance In the example below the image graphs sheets and database windows are arranged so that they do not cover each other This order is optimal when wanting to do intensity profiles or measure his tograms You can save such a layout in a workspace Please not that there is a default workspace for working with reports Use the Ctrl 2 key stroke to load this workspace First Steps Saving GUI configuration Step by step O analySiS Oy x File Edit Database Image Oper Measure Analysis Graph 30 C Module Special Window 7 Graphs 1 Sheet3 Roughness Standard OR x OR x Be LearmSIS_apl oO x Sheets Roughinews Standard gt p 4 A efis 1 imlaled Alx s t aee a alal ale ebale mE 100 Height mm E H 4 LeamSlS Roughness Aoughres Ready EIH Colorview I Fw ax fr oo ie a Step by step Saving GUI layouts as workspaces 1 Open documents of all the types you wish to have included in your graphical user interface GUI e g an image a database a measurement sheet and a diagram Close all other documents Use the Measure gt Histogram command to quickly create a diagram and sheet in addition to the active image e Press Alt 1 and Alt 2 to make both viewport and image manager disap pear from view 2 Arrange the windows optimally to your satisfaction within the GUI e Select the Special gt Pref
268. se archival and results documentation are all at your disposal in analySIS We think you ll find working with analySIS a tremendously satisfying experience analySIS is available in many various expansion versions and configurations This means that some functions described in this Step by Step introductory manual or in other documentation may not be included in the software package you have cho sen or vice versa some functions that are included in your package may not be described below Stop on by our website It is chock full of information including our ever growing range of products how to contact our customer service hotline all about our upcom ing workshops and seminars and much much more The software is protected by a dongle It is standard practice that a USB dongle which is to be installed on one of your PC s USB ports comes with the computer For PCs that don t have a USB port an LPT dongle is available on request e analySIS can neither be installed nor started without the dongle e The dongles are differently colored depending on which type they are USB Dongle LPT Dongle s s s Meaning unlimited single license black not limited time dongle which only unlocks the software for a available limited amount of time network dongle e A network dongle can be connected to any of the computers of the network Please keep in mind that before analySIS can be installed the driver software for the ne
269. sed by you from the Illumination method list e The online shading correction will immediately be used should correction images already exist for the current settings Should no appropriate correc tion images be available your image analysis program will automatically start a software wizard for the acquisition of correction images 8 Click OK to close the dialog box Logical input channel properties will be de New Channel fined in a single dialog box on several tabs For Duplicate Channels every different camera Configure Input configuration used you Delete Channel may define a separate l input channel Your im Configure Device age analysis program Help supports up to 100 channels Scanners and cameras a Set Input Fa with a TWAIN interface 4 may be operated via these input channels as well DA Colorview Ill u Puy 4 Calibrd Color iew Ill u Fv BY iia Colorview Iu Puy BY Ger Indu 18S 6g Acquiring images Optimizing display Background information A Z D O gt Q gt D indy lt ndu sunbyuoy Optimizing display Background information Configure Input gt The Configure Inout gt Display tab provides you with a number of possibilities for op Display timizing the way live images and snapshots are displayed on your screen These in clude Configure Input x Select Device x Available devices OF El Bs o15 View Firewire Camera A Colorview lu Fa 22
270. select the unit desired for the classification The unit you select will depend on the classification criterion If you re planning on classifying according to area for example you could select a unit of um 6 Click the Compute button to define the number and value range of each class The value range is determined by the minimum and maximum par ticle parameters e lf you have already detected an image you can allow a suitable clas sification scheme to be automatically calculated In the Compute Classification dialog box enter the criteria and the amount of classes and click the Auto button 7 Click the OK button to return to the Define Classification dialog box 8 If you wish to edit the class divisions interactively go to the Define Classi fication dialog box e To alter the color of a class select the line number of that class and select one of the 16 colors available in the Set color color palette e Togive names to classes leftclick in the Name field of the class Enter the class name into this field e To interactively alter class divisions of a class doubleclick on one of the numeric values and enter a new one 9 Click on OK to exit the dialog box Applying classification 1 Select the Analysis gt Classify command to divide detected particles up into classes 2 Select the particle parameter you wish to use to classify with in the Criteria list in the Classify group e g Area The parameter you use
271. sertion of images e an entry in the field is required e apicklist with possible entries is to be offered e the entry may only be an entry from the picklist e anew entry may be made in the picklist and or e the most frequent entry should be suggested as default value An organizational field belongs to the higher ranking database folder The organiza tional field contains information which can be related to all the documents within the database folder This can be for example customer and profit center All other database fields can be different for every single record However the orga nizational fields have the same value for each record stored in a database folder The table shows icons used to identify database fields in the Define Fields dialog box Predefined organizational field Predefined database field n User defined organizational field User defined database field Define organizational fields You can only define database fields if the database is opened exclusively Following the setting up of a new database the database is opened exclusively 1 Select the Database gt Administration gt Define Fields command gt The Available Fields list contains the organizational ID e g Project No and the predefined database fields 2 Click the Add New Field button You will find this button immediately above the Available Fields list gt The Add Field dialog box will be opened Here you define the new data
272. simply have to judge us ing your own eyes Creating 3 D surfaces Editing models Step by step e You can cut out the desired image structure using a frame in the height map Modify 3D Surface gt ROI this is how you create a model based on an image segment e Globally set frames Image gt Set Frame are of no use here e Height maps based on stereographs for example have a border whose gray value is constant Click the Modify 3D Surface gt Auto RO button to have this border clipped automatically e If you wish to compute a model based on one or multiple arbitrarily shaped image segments you need to define a mask image While pressing Ctrl drag the mask image onto the 3D window Activate deactivate the mask via the Modify 3D Surface gt Use mask check box Setting height 1 Make the grid visible to be able to see the scale graduation of the axes This is done by clicking on the Hide Bottom Grid button 3 D button bar so that it is not depressed 2 Click the Modify 3D Surface button Surface button bar at the lower edge of the 3D window 3 Enter the percental height of the brightest or highest pixel of the height map relative to the maximum value of length and width into the Height field e Anentry of 0 results in a model that is a plane At 100 the model s height equals its length width Low percentages yield flatter gently in clined models higher percentages more steeply inclined models 4 Select the Dis
273. sired measurement function You can measure as many values on the image as you like You end the measurement by either depressing the middle mouse button or the Esc key 3 Points Angle 4 Points Angle Rectangle Rotated Rectangle 3 Points Circle Circle with Center and Radius Ellipse Measurements EJ iij Halea als ole aoa Create Measurement Sheet Delete Measurement from Image Polyline Move Origin Arbitrary Line Magic Wand Horizontal Line Free Hand Polygon Vertical Line Fitted Polygon Touch Count Interpolated Polygon Point Closed Polygon Step by step This is how you measure distances and areas You want to make various distance and area measurements on an image 1 Load the image to be measured or acquire an image Warning j A correct image calibration is a requirement for a correct measurement 2 Click the Measurements Bar button located in the standard button bar to switch H to the measurements environment Alternatively you can use the Alt 4 key stroke or the Measure gt Measurements Bar menu command gt A button bar with all the measurement functions is shown next to the image manager e The image manager alters its appearance The Measurements tab serves as the measurement display and is activated The measurement display is still empty 3 Select the measurement function you would like to use from the measurement button bar Click the Arbitrary line button to measure any distance gt The pointer moves
274. size of the text object 8 Define a frame surrounding your text object in the Line tab gt Clear the Transparent check box and determine line width and color A number of line types are only available for the thinnest line width 9 If you wish to have image comment highlighted in color go to the Fill tab to de fine a highlighting color gt Clear the Transparent Fill check box and determine the highlighting color via the Foreground Color button 10 Click OK to close the dialog box Background information If there are any sheets open during insertion you will be informed via picklist about E Sheets Click this button in the Report Objects button bar to insert a sheet into a report Properties of sheet objects Sheets in record ob the open sheets Select the sheet which you would like to insert from the list If there are no open sheets insert a placeholder for the sheets The sheet object you insert when working in a report template in order to reserve space for a sheet is always empty e Selecting sheet cells your image analysis program will insert precisely those sheet cells of the measurement sheet that are visible within the sheet window This means you can alter the size of the window to clip lines and or columns Empty sheet cells are ignored at insertion You can make use of the autofilter functions located in the Edit menu in order to have specific kinds of data not shown Any filter you have set will be
275. t Pars 152 51 Bright Pas 154 04 Bright Par ae Bt We Siete How can I detect one result at a time 1 Select the Analysis gt Single Result command gt The pointer will appear within the image window gt The particles you detect will be shown in the image overlay 2 Leftclick on the particles you wish to measure gt The measurement parameters selected in the Define Measurements dialog box will be entered into a measurement sheet If a particle results sheet is already active your image analysis pro gram will append a single result to that sheet A new sheet will be opened if this is not feasible 3 Rightclick to terminate measurement Showing measurement results 1 Select the Analysis gt Define Measurements command to add the Feret Max particle parameter to the list of measurements 2 Select the Analysis gt Single Result command while pressing Shift 3 Leftclick on the particles of interest to you gt Your image analysis program will show the measurement parameters selected in the overlay Rightclick to end the export of the measurement results we o gt i ae if G Ay Image Analysis Editing detection interactively Background information Editing detection interactively Background information Use the Analysis gt Delete Particles and Append Particles commands if some particles have been improperly or not at all detected Example for editinga Following automatic setting
276. t in the Set Unit dialog box e Select e g uin the Scale list if you wish the calibration length to be shown in um Confirm by clicking OK 6 40 Acquiring images Calibrating inputs Step by step 7 Select the appropriate X Y ratio for your camera e Your camera normally has square pixels In this case enter the value 1 in the X Y ratio filter Select the Fixed check box 8 Set your microscope to the lowest magnification level available 9 Enter this magnification level into the Magnification field When using light mi croscopy you generally use the objective magnification 10 Click on the Snapshot button to acquire an image of the calibration specimen The image will be put into the active image buffer e Use the live image onscreen to position and focus the calibration speci men Simply click on the Acquire button first When you re satisfied quit the live mode by clicking on Snapshot 11 Enter the length you are using to calibrate with into the Calibration length field e The distance between the scale marks 30 and 80 in the example shown is 500 um 12 Select the Arbitrary option in the Calibration group 13 Now click on the Calibrate button gt The mouse pointer will appear within the active image 14 Position the mouse pointer at the starting point of the calibration length and left click 15 Then position the mouse pointer at the final point of the calibration length and confirm by leftclicking
277. t the overlay object has an automatic frame meaning frame size cannot be interactively altered gt The newly inserted text object remains selected within the image The overlay of this im age consists of 4 over lay objects three text objects of varying for mats and a bitmap ob ject on the right All overlay objects are on the annotation layer The dynamic scale bar is not an overlay object Inserting and formatting arrows 1 Click the Arrow button 2 Leftclick to define the initial and terminal points of the arrow in the image win dow 66 100 Processing images Editing overlay Step by step gt Any and all current selections will be canceled Your image analysis program will insert the arrow selected into the over lay The arrow s initial appearance upon insertion is determined 3 Click the Object Properties button to format the arrow you decide the arrow s color type of line line weight and arrow style 4 Click the Apply button to assign the arrow the properties selected 5 Once satisfied with your arrow s appearance close the dialog box via Close Loading any bitmap into the overlay 1 Click the Load Objects button gt The standard dialog box for loading files will be opened The Files of type list provides you with a number of image file formats to choose from BMP ICO EMF along with the file format for overlay files OVL 2 Select the Windows bitmap BMP entry Select t
278. t window Select e g the report name located at the bottom of the Window menu in the list of files 4 Select the image object and click the Sheet button located in the Report Objects im button bar and pull open the sheet object gt Should you have loaded numerous sheets the Available Sheets dialog box opens Select the desired sheet and confirm via OK gt Your image analysis program will insert all lines and columns of the mea surement sheet into the report that are visible within the sheet window Cells that are without content will be left out 5 Click the Ungroup button in the Order and Group button bar to be able to edit the sheet within the report gt What to do if the button bar is not available Use the Special gt Edit Button Bars command To have a button bar dis played select the check box next to the name of that button bar gt Asheet that is inserted into a report is comprised of a group of text objects The grouping that had kept the individual cells together will now be taken apart You will thus now see the marking symbols around each separate text object gt You can now e g rename the sheet or the columns add a comment on individual measurement values or have certain cells of the sheet highlight ed in color 6 As needed you can edit the sheet Doubleclick e g on the sheet header to rename the sheet c6L 194 Report Generator Report objects Step by step 7 Once editing is completed
279. t you wish to move in relation to another object gt Gray selection markers will appear around the object selected 4 Keep the Shift key depressed and select the reference object gt Both objects now have selection frames around them The selection mark ers of the object you last selected are gray and the other one s selection markers are white 5 Use the first buttons of the Align button bar to align all objects that have white selection markers in relation to the object that has the gray selection markers Click e g the Center Horizontal button to move the object selected to the left or to the right until all center lines are in alignment i e in the same position gt Objects will only be moved to the edge of the page and no further Image Objects Background information Image object Inserting an image FS object Inserting images Warning l Sequence when in serting Image types You cannot insert images into a report directly You have to first create an image ob ject to define the size and position of the image as well as its properties After inser tion of the image object the image object remains empty You can identify an empty image object by the fact that the area reserved for an image is hatched Click the Image button located in the Report Objects button bar to insert an image object into a report Use the mouse to drag an image from the image manager or directly from an image database onto a
280. tatistic values are always written to a separate sheet they cannot be writ ten to a sheet together with the measurement values This is how you work with the statistics functions 1 Carry out an area measurement on numerous images gt The Statistics for Area group located in the measurement display is up dated after each executed measurement By default it contains the amount of executed measurements the mean minimum and maximum area measured and the standard deviation 2 In the tree view select the Perimeter measurement value gt The data in the measurement display no longer correspond to the mea sured areas but to the measured perimeter 6LL 120 Interactive Image Measurement Measuring Arbitrary Structures Background information In addition to the mea surement sheets you can also export a sheet with measurement sta tistics 3 Click the Define Statistics button You will find the button in the measurement display above the tree view gt You will find all available statistic parameters in the Define Statistics dialog box You will find an explanation to each parameter selected All of the parameters which are currently selected are shown in list on the right entitled Current You can always alter this selection without having to repeat a measurement 4 Should the statistical values Minimum and Maximum not be shown select the parameter Minimum and Maximum located in the Define Siatistics dialog box and
281. te Web site with your permission Read our privacy policy Can Windows connect to Windows Update to search for software O Yes this time only Yes now and every time connect a device amp No rot this time Click Next to continue Grech Cancel Warning i The correct dongle driver can only be installed during the installation of analySIS 4 Close the Found New Hardware Wizard dialog box by clicking the Cancel but ton Keep clicking the Cancel button until the dialog box disappears 5 Place the analySIS installation CD into the CD ROM drive gt The setup program will start automatically unless you have deactivated the autorun function If so start the setup exe file manually via Windows Explorer Step by Step analySIS Installing analySIS Step by step When you insert the in Stallation CD the setup menu will come up om OLYMPUS Your Vision Our Future amp analySIS FIVE Setup Oy x analysis FIVE Documentation Acrobat Reader Network software protection key Explore this CD _ Olympus Soft Imaging Solutions Website S Quit Digital Imaging Solutions Based on the analysis Platform Olympus Soft Imaging Solutons 6 Select the analyS S FIVE option in the setup menu to install or update this soft ware 7 An installation wizard guides you through the entire software installation Simply follow the onscreen instructions and select the relevant entries
282. tection interactively 159 Filtering class results 165 Image preparation 142 Possible stumbling blocks 166 Showing measurement results 158 Display Configuration 19 Display Properties 18 Document with Subdocuments Database 89 Dongle 5 Dual Screen System 19 E Edit record 74 Emboss Filter RGB Studio 109 Equalize contrast 102 Exposure time 34 Exposure time correction intX 26 Express database 58 False color display 139 Filtering class results 165 Frame 147 To set a frame 148 Full Screen 126 Full Screen Mode 126 G Gallery View Database 79 Gamma Correction 104 Gamma Filter RGB Studio 109 Graphical User Interface 12 GUI 12 H Histocontrast Filter RGB Studio 109 Histoequalize Filter RGB Studio 109 Histogram 101 145 How to install the software 6 HSI 103 Hue Filter RGB Studio 109 Identifying Particles 157 Image buffer box 12 Image buffer for image acquisitions 41 Image compression 48 Image file formats 48 Image information 43 Image Manager Measurements Tab 113 image name 41 How to change an image name 44 Image scaling 32 Image Sharpness 107 Image types 15 Image window 14 Index Activate image window 17 Adjust Window 20 Images Acquire 25 Calibration 38 Delete 50 Image types 15 Print 50 send 53 Storage 41 48 This is how you acquire images 34 To load images 16 Input 27 Calibration 37 Configuring 26 Configuring the input 28 Duplicating already existing input 28 Macros 42 Th
283. tensity calibration How to measure length or distance height distance and position 1 Enlarge the 3D window as well as the model so you can define measure ment points as precisely as possible Leave some space along the lower edge of the Graphical User Interface GUI to be able to see the measure ment sheet during measurement 2 Select the Measure gt 3D Measurements gt Polygon Length command to define and measure an arbitrary polygonal length gt Your image analysis program will create a new measurement sheet called 3D Polygon Length The mouse pointer will appear in the 3D window Points and lines of any previous measurement will disap pear 3 Use the left mouse button to define the polygon s points to be measured gt The status bar will show the coordinates of the point last clicked on Creating 3 D surfaces Measuring models Step by step gt Straight lines through three dimensional space join the points de fined To measure a length along the model s surface define many closely positioned points 4 Any points set erroneously can be deleted one at a time successively This is done by pressing Shift and leftclicking 5 If you need to move the model surface while defining your polygon length you may do so using the following Shift arrow keys move rightward or leftward upwards down wards Shift Page Up reduce in size or enlarge PageDown Ctrl arrow keys rotation tilt t
284. ter When using the image generator save the image to an image database and then insert the Image Comment database field to a database object Step by step Change an image name after it s been acquired 1 Doubleclick on the image buffer to change the name of the image in the active image buffer gt The Image Information dialog box will be opened e The Genera tab has all the image information automatically read out at im age acquisition e The Camera tab has all the data of the logical input channel the image was acquired with 2 Enter the new image name into the Image name field in the General tab 3 Enter any comments on the image you wish to make and evaluation thereof into the Comment field e Use key words of the image comment to query the image in an image da tabase if you have archived it in one of course 4 Confirm by clicking OK gt The image buffer will automatically show the new image name Acquiring images Showing scale bars Background information gt This image name is now the default name and will be proposed when you go to save the image as an image file or as a record to be inserted into an image database Read in magnification automatically at image acquisition Add the Image gt Set Magnification command to the logical input channel TERK Colorview ll u Fw 1 Doubleclick on the input channel icon in the status bar Soleil Iu PAY gt The Configure Input dialog box for the active logical
285. tered settings transferred to the im age Possible stumbling blocks during a particle analysis Automatic Threshold Value Defining detection If the results of a particle analysis appear differently than what you had expect ed check the following points You can automatically calculate the threshold value for gray value images e Automatically calculated threshold values are only then active if you click the Auto button located in the Manual tab which is located in the Image gt Set Threshold dialog box The manually set threshold values remain active if the button is not clicked Hence not the desired particles will be detected The background must be correctly defined during an automatic threshold setting For example if you would like to detect a light particle on a dark background select the Background gt Low option located in the Image gt Set Thresholds gt Auto Settings tab If you want to detect a dark particle on a light background select the Background gt High option Please note The Background gt None option should not be normally used for an automatic particle detection In this case all of the gray values of an image are matched to a phase and the entire image is detected No particles or fewer than expected have been detected e Clearthe Use ranges check box located in the Analysis gt Define Detection gt Detection tab In doing so you deactivate the particle filter which is even tually still
286. th the left or top frame border e Exclude any particles touching the frame or ROI will not be detected Detection area Fra me Border Particles p 8 Cs z we Ot DA a Include A Exclude e Adjacent borders 4 Two pixels belong to a single particle if one of their four sides touch e Include diagonals 8 Two pixels belong to a single particle if one of their four lateral edges or diagonals touch E E Adjacent borders 4 Include diagonals 8 iz lis tT Be 3 Particles 1 Particle Holes are continuous gray value ranges within a particle but are not part of that particle These holes are either detected as such or ignored How holes are treated affects particle area Defining detection 1 Select the Analysis gt Define Detection command gt The Define Detection dialog box has three tabs for defining detection and classification parameters 2 Select the Detection tab to set particle detection parameters 3 Enter the minimum number of pixels which may be detected as comprising a particle into the Minimum field of the Particle filter group LGL 152 Image Analysis Detecting particles Step by step Enter a value of 10 into the field for example to have only particles detect ed that have an area of at least 10 pixels or more gt This is an excellent way to exclude particles comprised of very few pixels Detecting these particles can be rather pointless Ente
287. that no other action is allowed in the report as long as your im age analysis program is waiting for the definition of an object You will no tice this mode by the fact that the object button located on the Report Objects button bar is now engaged 4 Defined the object on the report page For example keep the left mouse button depressed and drag the rectangle to its desired size e Please note Some objects might require numerous mouse clicks when de fining them End the definition of such an object by clicking the right mouse button gt The object is inserted as selected so that you can edit it right away Once again the Select Objects button which is the first button on the Report Ob jects button bar is engaged e However you can alter the position and the size of the inserted object any time 5 In order to format the object rightclick and select the Properties command Aligning objects in relation to one another 1 Show the Align button bar should it not be visible e To do this rightclick on any place within the report to open a context sen sitive menu All button bars having to do with report generator are listed be neath the Button Bars entry Select the Align button bar Report Generator Image Objects Background information 2 Position an object at the position desired within the report This object is to be the reference object for the positioning of the other objects 3 You now select the first objec
288. the Browse button next to the Destination file field Report Generator Report objects Background information 3 Select the directory for the RTF file in the Save RTF dialog box Enter the name of the RTF file into the File name field Click the Save button to return to the Ex port RIF dialog box gt The complete path and file name of the RTF file is now located in the Des tination file field Note that the RTF file has not yet been saved D Determine the resolution of the images in the RTF file and thus the file size of the RTF file in the Reduce image data group If you are planning on sending someone the report by e mail then it makes sense to keep file size as small as possible Select the Use JPEG compression check box U1 Enter 60 into the quality field This quality value determines the degree to which images are compressed low percentages mean a correspondingly high degree of compression gt The JPEG compression reduces the file size of an image but also gener ates typical image artifacts The more you compress an image the greater the loss in image quality JPEG artifacts are generally not visible in a print out at 60 6 Initiate exporting by clicking on OK gt The resulting RTF file you can now e g load in MS Word or send to someone by e mail The layout of the report remains completely un changed in MS Word e The file size of RTF files can be very large You can reduce the file size by saving
289. the measurement display gt The selected measurement value disappears from the tree view The re spective measurement object is simultaneously deleted from the overlay e Please note that you cannot delete the measurement values by deleting the image overlay The image overlay is recreated from the measurement files as soon as the image has been reactivated or new measurements have been added 5 It is sometimes easier to delete a value from a measurement by simply identify ing it on the image In this case click the Delete Measurement from Image but ton on the measurement button bar gt The pointer moves to the image window 6 On the image click on all the measurement objects that are to be deleted gt All deleted values disappear from the overlay and from the tree view 7 Depress the middle mouse button or the Esc button once you have deleted all the values you wanted to delete This is how you delete an entire measurement 1 Select the image names from the tree view located in the measurement display 2 Click the Delete Measurement button located in the measurement display gt The selected entry appears from the tree view All measurement values which belong to this image are deleted e You only delete the measurement value with this function not the image The image is continued to be normally loaded into the image buffer In the measurement dis play select what you would like to delete Image Manager deran
290. the report in MS Word as a Word document in DOC format Printing the report 1 Select the File gt Print command to print out the finished report gt The Print dialog box is context sensitive This simply means that the func tions being offered by the dialog box depend on what document is active Before you print a report you have to activate this dialog box 2 Select the Full image option from the Images group within the Print dialog box 3 Select the All option from the Print Range group to have the report printed out in its entirety Start printing by clicking on OK Report objects Background information Report objects A report page usually includes various kinds of objects These may involve image and text objects as well as graphic objects For each object there are individual char acteristics which can be defined which are different for each object type A certain object type the record object can consist of numerous other objects You can define individual object templates for record objects In doing so you not only create a wealth of different record objects but also guarantee a uniform appearance of the record objects in different reports Placeholder Several objects serve as placeholders Image objects and record objects are typical placeholders These objects are usually defined in a report template If you then cre ate a report based on this template the placeholders are filled with concrete images Record o
291. ticles so that they are distinguishable from image back ground Defining this range is referred to as setting thresholds The thresholds are comprised of the lowest and greatest gray color values There are two ways to set thresholds for gray value images e Set the threshold values in the histogram interactively Set Thresholds gt Manual tab e You may also have threshold values calculated automatically from the his togram Set Thresholds gt Manual tab Auto button When using color images you define the threshold value interactively in the im age Histogram A histogram displays the number of pixels versus the corresponding gray val ues You use this gray value distribution of the image to define the gray value range for particle detection Setting a Before beginning automatic particle detection set the gray value color value Step by step Setting thresholds 1 Load the image you wish to analyze into the active image buffer e The following description of the particle detection is based on an 8 bit gray value image Gt 146 Image Analysis Detecting particles Step by step Cut ends of carbon fibers are shown in the image above The fibers gray val ues depend on the angle of the cut cj In the example shown the histogram below has three gray value peaks that clearly correspond to image struc tures The dark background is somewhere in the vicinity of the gray value of 85 The gray values of the pa
292. tion The entire image is analyzed by default Your image analysis program also pro vides various possibilities for restricting image analysis to a specific area within an image You can set either frames masks or ROls You decide what detec tion area you use in the Define Detection dialog box Frame TEE A frame limits image processing and analysis functions to a rectangular area fa E within the image This frame is a global setting and is then valid for all images loaded and several image analysis functions ROI oO A ROI Region Of Interest is an area of arbitrary shape within the image It must be defined for each image ROIs are only valid for particle analysis ROIs can however be transferred into a mask and thus be used for other image analytical functions To transfer a ROI select the Analysis gt Draw ROIs gt Into Mask com mand Lvl Image Analysis Detecting particles Step by step The Define ROIs dialog box provides you with tools for defining and managing ROls drawing a polygon drawing an interpolating polygon CAEC drawing a polygon freehand yp OO ee a rn Shift drawi drawing a rectangle C drawing a rectangle of arbitrary orientation combining two ROls into one ca ROI based on a detected particle virtual ROI Shifting ROI selected from the f Deleting ROI selected from the active ROI list active ROI list Mask A Mask is a binary image which can be superimposed on the original image for 33
293. tive Image Measurement Create measurement sheets Step by step ale gi Clear the One sheet per image check box to write all the measured values to one sheet Confirm by clicking OK gt The measurement sheet is created and displayed In order to make the measurement sheet visible and to avoid having it covered by the image your image analysis program automatically returns the image window to its Original size 10 After the measurement has been completed release the Measurements Bar button gt The measurement button bar is once again hidden This is how you acquire a new image with a camera for each measure ment A series of images are to be sequentially acquired Distances are to be measured on all the images 1 Use the Special gt Preferences command In the Images tab select Image buffers All entry from the Image acquisition gt Sequence list Close the dialog box by clicking OK gt Your image analysis program now automatically jumps to the next image buffer before each image acquisition This prevents an already existing im age from accidentally being deleted during an acquisition 2 Click the Measurements Bar button located in the standard button bar to switch to the measurements environment 3 Maximize the size of the image window so that you have the largest amount of space for displaying the image possible 4 Acquire an image click the Acquire button to display the camera image live In the live image
294. to classify with is entirely up to you e Select No classification in the list of classification criteria if you do not wish to have particles divided up into classes The class parameters will then refer to all the particles that are detected 9 L 164 Image Analysis Detecting particles Step by step 3 Select the classification scheme you wish to use in the Class list This list will show all classifications that can be used with the unit selected e Should a suitable classification scheme not be available click the Classification button to create a new classification scheme or to edit an already existing one 4 Click the Execute button to have the classification applied to the image gt The particles in the overlay will be divided up into classes and shown in their class color Any particles that do not belong to any of the class es will remain crosshatched 5 If classification does not produce the desired results then feel free to try out other classification schemes before generating a sheet for your results 6 Click on OK to close the dialog box The same image using two different classifications Particles classified accord ing to shape left The same particles classified accord ing to size right ts Particle_Area ij Shape_Factor ID Class Particle Count Mean Area a 0 974 56 Select classification parameters and export results 1 Select the Analysis gt Define Measureme
295. to your needs when working with report generator define window width of the report window and of the database win dow such that both windows may appear at the same time Position both win dows so they do not overlap Place the button bars which belong to the report generator to the right or the left within the user interface not below the standard button bar at the top If the button bars are positioned below the standard button bar the display of the whole Graphical User Interface will move up each time you switch documents If you are inserting images from only one database then you can increase the w Report Generator Planning report templates Step by step amount of space for report generator significantly by minimizing both the image manager and the Viewport manager while you edit a report To minimize the one and then the other use the following keyboard shortcuts Alt 1 and Alt 2 Reference Page Create reference pages for all elements that you use fre quently in your report template This could e g be a group comprised of an image object text object and lines Text objects which can be edited cannot be defined within a record object This is why you define a record object along with a text object on the reference page Define all the elements that can be copied faster than they can be created from scratch e g graphic elements you have created on your own Gog 206 Index Index Numerics 3D surfa
296. tor Inserting sheets Step by step Unlike the sheet objects which are directly inserted into the report the acquired sheet cells are independent of the window size of the sheet Use this possibility if your measurement results are always written to a sheet in the same form in order to determine the sheet cells which are relevant for you Sheet cells as field Many special Add Ins deliver standardized measurement sheets which are always objects constructed the same way Use a special field function to acquire individual measure ment results i e the G value of a grain size analysis into the record object The Sheet Cell field is automatically included in the list of database fields This field has additional object properties You can exactly specify the desired sheet cell in the Record Fields tab A sheet is a group of in dividual text objects Therefore you can change the appearance of a sheet from sheet cell to sheet cell PhaseAnalysis w PhaseAnalysis O m fe e O63 42 13 45 Step by step Insert and edit open sheets directly into a report 1 Load the sheet you want to insert into a report For example use the Measure gt Histogram command to create a sheet 2 Now maximize the sheet window to do so click the middle button in the upper right corner of the sheet in the document header This will enable you to have the greatest number of sheet cells inserted into the report 3 Activate the repor
297. twork dongle has to be installed first The Setup menu includes an op tion for installing the driver software for the network dongle Installing the network dongle 8 Step by Step analySIS Installing analySIS Step by step Step by step Warning Install the image analysis program before connecting the camera with the FireWire slot This sequence is necessary to avoid having the operating sys tem install the wrong camera driver The camera drivers which are required for the operation of the cameras are installed together with the software Warning The installation of the hardware is described in the corresponding installation manu al The notes on hardware installation in this chapter apply solely to Olympus Soft Imaging Solutions FireWire cameras Installing the analyS IS software 1 Turn on your PC and if necessary start up the operating system 2 Close any and all application programs 3 Insert the software protection key dongle into a USB port of your PC gt The Found New Hardware Wizard dialog box will appear The operating system will then try to install a driver for the dongle As soon as you have in serted the software pro tection dongle the Found New Hardware Wizard dialog box will appear Found New Hardware Wizard Welcome to the Found New Hardware Wizard Windows will search for current and updated software by looking on your computer on the hardware installation CO or on the Windows Upda
298. ue color image Do not use the Oper gt Change Bit Depth gt To 8 Bit because this command alters the image informa tion so that it is no longer suitable for a particle analysis Offset correction 1 Load the image you wish to correct into the active image buffer 2 Select the Oper gt Define Shading Correction command 3 Click the Window button to define the image segment for the preview e Use the left mouse button to set position and size of the preview win dow Rightclick to confirm your settings gt The Preview check box will be selected The preview will then contin ually show how parameter alterations affect the image segment The upper left image shows spherical polystyrene struc tures Both the spherical structures and image back ground get darker looking from left to right It is there fore not possible to set thresholds only for particles After shading correction up per right image illumination is even and thresholds can thus be set Image Analysis Image preparation Step by step 4 Select the Multiplicative option in the Assumed deterioration group 5 Select the Source 1 option in the Source for shading image group to have the correction image calculated based on the image being corrected 6 Select the NxN average filter in the Preparation of shading image group 7 Set the parameters for this filter in the NxN average filter group e g set the number of iterations to 3 and the size of the f
299. ues are directly used with images whose image inten sity has already been calibrated When using calibrated height maps each gray value corresponds to a specific object height You can calibrate the height map with the Image gt Calibrate Image gt Image Intensity or Image gt Define Image Calibration A calibrated height image is required for the following e to obtain a model that is true to scale e if height is not in proportion to pixel intensity e tobe able to measure lengths or distances Creating models 1 Load the height image of the object s surface into an image buffer Load the texture image if available into another image buffer 2 Activate the height image Select the Oper gt 3D Surface gt Create com mand 3 D surface generated via height map DP Creating 3 D surfaces Creating models Step by step gt The 3D window will be opened and the model displayed Only one model can be shown at a time ay Surface3D wad O Se en Bl l ee A 3 D button bar amp 3 D Position button bar co 3 D view area 3D Navigaton a Y Surface button bar HUZ od Eal l 3D Navigator 3 Drag amp drop the corresponding texture image onto the model e You wish to make the texture image disappear select the Surface button bar gt Modify 3D Surface gt Encoding gt Height coded op tion e You wish to enlarge the 3D window press Alt 1 and Alt 2 to get rid of both the viewport
300. uired fields are Client P indicated by an excla mation point G9 Archiving Images Insert data Background Information Insert data Create a new database folder Background Information Insert database folder Database folder name Step by step There are several options for creating a new database folder 1 Menu command open the Database gt Insert submenu To set up a new data base folder select the first command in the submenu This command is different for each database and reflects the organizational ID of your database 2 Button in the database window In the database window s button bar click the lt Organizational ID gt insert 3 Context menu activate the database window and click the right mouse button to open a context menu Open the Insert submenu Select the first command in this submenu 4 Drag amp Drop drag the image that you want to insert into the database from the image manager onto the database name in the tree structure of the database window You will be asked to set up a new database folder Confirm the message by clicking Yes The standard name for a new database folder is defined in the database settings Use the Database gt Administration gt Settings command to view the settings for the active database The database must be opened exclusively if you want to alter the settings You can use any fixed text and two wildcards e The lt organizational ID gt is predefined as a fix
301. und information e Working with magnifier Select the automatic zoom factor for the image in the image window A large im age will be shown greatly reduced in size The magnifier view in the viewport manager shows a magnified section of the image beneath the current position of your mouse The current position of your mouse is shown by cross hairs in the magnifier You can set the zoom factor for the magnifier by clicking on the image in the viewport manager with the right mouse button and selecting the de sired zoom factor from the context menu Note You can move the image under the magnifier s cross hairs with the arrow keys of your G keyboard during measurement Use the arrow keys to set a point as accurately as possible The magnifier in the viewport manager on the left magnifies the im age section under the current position of your mouse right E Jal Dz f gt S gt S gt SSre ke Altering In the measurement display click the Measurement Properties button to change the Measure program s general settings which have to do with interactive measurements ment e Clear the Continuous measurements check box when wanting to use various Settings measurement methods or simply executing a single measurement The pointer appears in the image only for one measurement After a value has been mea sured the pointer returns back to the measurement button bar e You determine which files are to be written to the image o
302. ut the micro scope together with the image Some add ins also create additional tabs with special image data in the Image Information tab Please note Save your images in TIF format so as to save all additional data togeth er with the image Image number Imai e Manager Ei pH gt 2 kc J Dest Image buffer box katalysator Image Information General Camera mage name Tw File name LAT emp slmages 20071 001 tif Image butter 1 Frame 1 7 1 Memory size 14585 KB File size Created 01 10 2007 15 13 Channel Coloryiew II u Pa Magnification 1 x Resolution 2576 w 1932 s 24 Width 6 758 mm Height 6 569 mm Image intensity image name ecer List la Comment Cancel Help ep 44 Acquiring images Saving images Step by step Nhe ea A tains the settings of the itladaaddaiatadadd input channel during ac General Camera quisition Camera type Color ier Ilu F Lett margin 0 Fisel Top margin 0 Pixel Right margir 0 Fisel Bottom margin 0 Pinel Binning 3 1x Binning x Exposure time BU m Gain corrected Ho Offset corrected No Bad pizel comected Mo Cancel Help Print image You can print the image comment together with the image This can be done either comment by using the File gt Define Page Layout command or by using the report generator that is integrated in your image analysis program In the page layout acquire the Comment wildcard in the header or foo
303. ve a successful particle de tection the particles must clearly stand out from the background All detected particles will be automatically measured You can choose from a wide array of measurement parameters You must do the following steps when executing your first particle analysis e Set threshold value see page 145 e Define detection parameters and execute detection see page 151 e Select particle parameters see page 153 e Define classification schemes see page 163 e Classify particles see page 163 e Select parameters for a class measurement see page 164 e Export results If you analyze similar images the existing settings will be adopted You can also save all the settings and thus use them again anytime The number of steps for each detection afterwards is thus reduced e Setting thresholds LVL 142 Image Analysis Detecting particles Background information Executing detection e Export results Image preparation Background information Shading correction Separating particles Color Separation Step by step Shading correction is for equalizing non homogeneous image background This kind of image interference occurs e g if image illumination is not homogenous during the acquisition of an image Shading correction may be necessary before you conduct particle detection to ensure that gray or color values and image structures are clearly correlated Before particle detection neighboring particle
304. verlay during a mea surement in the Show labels group e You determine the color of the measurement objects located in the image over lay in the Label style group The font size and font thickness of the measure ment overlay can be altered in the View tab Origin of There are some measurements where the coordinate origin is important Such a the Coordi case is the measurement using the Poinis button The measured point position is giv nate en corresponding to the origin of the coordinate system System By default the origin of the coordinate system can be found in the upper left corner of the image Click the Move Origin button to move the coordinate s origin to a de sired position on the image All values already measured are adapted to the new or igin Gg L 126 Interactive Image Measurement Optimizing work environment for measuring Background information The coordinate origin is shown by a red coordi nate system in the im age s overlay PS images 5 Nodular Graphite In the measurement settings mark the Use inverted Y axis check box to place the origin of the coordinate system in the lower left corner The new position of the coor dinate system will only be taken into consideration for newly acquired images The origin of the coordinate system remains in the lower left corner for already exist ing images As it is mirrored with respect to the X axis the resulting X values are pos itive and the resulting Y
305. view to switch to that image Select a measurement function from the button bar and measure the desired structure The new measurement will be attached to the already existing measurements Each interactive measurement also creates an image overlay which shows the mea sured object The measurement overlay is linked to the measurement values and is automatically recreated from the measurement data when loading an image or when continuing an interactive measurement Should you have edited or deleted the mea surement overlay the respective alterations will be reversed This makes sure that the measurement overlay and the measurement files remain consistent Be sure that you cannot alter the measurement data by editing one of the measurement objects in the overlay This is how you delete single measurement values 1 Load the image whose measurement values you would like to delete 2 Click the Measurements Bar button located in the standard button bar to switch to the measurements environment 3 Select the value you want deleted in the Measurements tab Interactive Image Measurement Save Load and Edit Measurement Results Step by step e When measuring certain objects such as a circles numerous values are measured simultaneously Please note that it is impossible to delete indi vidual values with the delete function You do however delete the entire measuring object that was measured 4 Click the Delete Measurement button located in
306. which will be added to a project in the database the method of investigation should be included For images existing organizational fields are also to be shown in the inser tion mask for information purposes 1 Open the database exclusively e Select the Database gt Open command In the Open Database dialog box select the database file and mark the Exclusive check box You can recognize the database file because of the APL file name extension Define Fields 2 Select the Database gt Administration gt Define Fields command 3 Click the Add New Field button 4 Change the standard name of the new user field in the Field name Enter for example Investigation method as the new user field 5 The Data type list offers various types of data Select the Memo option when you want to enter a lot of text in the comment field 9 64 Archiving Images Define a database Step by step With this step you 6 The Organizational field check box should not be marked This way you can decide that the new allocate a different method of investigation to every record that is added to a field is not to be an database folder organizational field 7 Glose the Add Field dialog box by clicking OK gt The new database field has then been set up and will be displayed in the Available Fields list f gt All of the database fields are characterized by an icon in the Define Fields dialog box The new database field will be prefixed by th
307. will also have been supplied with other manuals as well as these step by step instructions See more tips by using the gt Welcome Welcome command Welcome to Did you know lt iz possible to load images by a Drag kDrop procedure Drag the image from the dialog box Oper Image on the image butter Previous Tip Next Tip T Show this Welcome Screen nest time you start this program 10 Step by Step analySIS Any questions or problems Step by step Step by step We want to hear from you If you have any questions or any problems you re having difficulty solving on your own even after consulting the relevant documentation then contact our customer service preferably by e mail Our customer service representatives will be more than happy to assist you 1 Start your image analysis program 2 Try and specify when and under what exact conditions the problem you re hav ing occurs e Ideally you should try and be able to reproduce the problem error This fa cilitates our customer service finding the source of the problem and thus a solution 3 Make an exact note of any possible onscreen error messages involved e Orsimply make a screenshot of the message s All you need to do to get a snapshot of the active window is to press Alt Print This copies the ac tive window to the Windows clipboard Then you can easily include the copied window in an e mail by pressing Ctrl V e Oversize
308. will find various types of measurement objects in the tree view 2 The list contains all of the measurement pa rameters which are at your disposal The mea surement parameters are shown for the types which are marked in the tree view 3 The Selected Mea surement list shows which measurement pa rameters are to be shown in the measure ment display and in the results sheet Types of Measurement Objects Sequence of active parameters Step by step Interactive Image Measurement Measuring Arbitrary Structures Step by step Select Measurements All C Gray Value Max Density Peed De Gray Value Mear Density a ies C Gray Value Min Density Get Default J Pai Ce Gray Value 2D eY Denei Ce Gray Value Variance Density File OIH Green Density CO Hue Density Hep Density IH Integral Intensity Gray Value bl Density Selected Measurements Court Group of points Point s Faint Point Point Length Line Value Angle kd The integral image intensity is the sum of all the intensities of a particle multiplied by the pixel area For a particle containing regions of highly differing density this method will produce a better estimation than Integral Intensity Gray Value Mean as long az the variation i not caused by noize or by the imaging process All measurements are divided into five different types points point groups lines an gles and 2D objects Each type has de
309. wn in the overlay in the Measure tab e Font size font size for particle labels is determined in the View tab in the Overlay group e Sheet the settings in the Sheet group also apply to particle results All results of a particle analysis which are written into the overlay can be edited just like any other overlay object Simply disable the lock on the data layer so you can begin editing Overlay gt Layer gt Lock Data Layer The Define Detection dialog box has a third tab with general settings on how re sults are displayed e Have class results for each ROI computed separately incl separate sheets This setting affects a number of class parameters Image Analysis Classifying particles Step by step e Values in the results sheet can be shown in the color of their respective class e You can have all shape factors greater than 1 set to 1 Step by step Defining a classification scheme oo 1 Select the Measure gt Define Classification command to define a classi fication scheme the way you need it 2 Select the Show sample objects check box to be able to judge the size nec essary for the classification gt The current overlay will disappear from view and your image analysis program will show a number of sample objects for visual reference purposes 3 Enter the name of the classification into the New Classification field 4 Click the New button to create the new classification scheme 5 Click the Unit button to
310. x e for an overview of the images loaded e for rapid access to image information such as its size and image type Saving GUI configuration 21 First Steps The GUI User Interface Background information e to activate image buffers The icon area e is for printing archiving or saving images one at a time You can hide the image manager to create more room for other windows for exam ple To do so use the Alt 2 key stroke 7 analyS S Menu Bar a Oper Measure Analysis Graph 3D C Module Special Window Viewpor Manager 1 Liver Tissue2 Image Manager gt i ie rc Dez Src 2 gt Sim C I CIVE iera 16 Bit Display 1280x1024x16 SS Active mag a 0 3D Suttace Mouse Tissuel H G act 2 L 40x 512 24 E G ADDA p Vickers Hardon O Analysis 3 1i 758 x 566 x 24 Neurons5 A E 1024x1024 16 Image Buffer Box WATE gjeo ae iS E ta Image Button Bar image Di n mee 3 m maga 8 a a e 2 m m gt meee 3 L 14 First Steps Loading images Background information Document Area Documents can only be displayed within this area Each document is opened within a separate window Your image analysis program supports the following document i Diagram Sheet Graph am oma Image window The image window is a special window for viewing either loaded and or live images Itis possible to view up to 25 images simultaneously To display them the
311. y calibrated E Adding zoomed image segments Detail Zoom 1 Insert an empty image object 2 Drag a large image either from the database or from the image manager onto the image object 3 Select the image object and click the Detail Zoom button located in the Report Objects button bar gt The pointer will appear within the report window You are now only able to move the mouse pointer within the image object 4 Now define a rectangular segment within the image e Keeping the left mouse button depressed move the mouse to form a rect angle within the image Release the mouse button once the rectangle is the size desired gt Your image analysis program will select the image segment selected and will automatically add another image object showing the image detail se lected gt Auxiliary lines provide a visual guide from the corners of the detail image to the corners of the image segment making it easy to see the visual cor respondence between the image segment and the detail image 5 Changing the size and position of the detail image Report Generator Record objects Background information e In order to position the detail image you move the mouse pointer onto the detail image As soon as an arrowed cross symbol appears at the mouse pointer you can press the left mouse button to pick up the detail image and move it to the spot you want to have it In order to alter the size of the detail image you first select the d
312. y the unmodified nethasp ini file to the server s c winnt or c windows Windows directory You will find the nethasp ini file in the program HASP Net work Help directory gt With the help of the nethasp ini file analySIS can then also be installed on the PC into which the network dongle has been inserted In this file the 127 0 0 1 entry is a reference to the PC itself Installing PDF documentation 1 Select the Documentation option in the setup menu to have PDF documentation files copied onto your PC s hard drive in full or in part 2 Simply follow the onscreen instructions and select the documentation desired gt A program icon that looks like a book will appear within the program folder selected This is a link to the documentation files that were just installed 3 Select the Quit option to exit the setup menu e To start up analySIS and or the documentation you had installed simply doubleclick on the corresponding icon s e Via the setup menu you can copy delete additional parts of the documen tation to from your hard disk Any questions or problems Background information Other All documentation is also available as PDF files on the analySIS installation CD To documentation select the files you wish to have copied onto your hard drive go to the setup menu These files can be viewed onscreen and printed out using Acrobat Reader by Adobe comes with analySIS Depending on the scope of your order you
313. yers currently being shown Load Objects loads bitmaps icons metafiles or complete overlays from an existing file into the overlay of the active image Save Objects saves all selected overlay objects to an overlay file copies selected overlay objects from one image into another Cut Objects Copy Objects Paste Objects or within the same image Please note that overlay objects cannot be copied using the Windows clipboard L6 98 Processing images Editing overlay Background Information Burning Overlays Bring to Front arranges overlay objects in the order desired in front of be send to Back hind etc Arranging overlay objects is only possible for over Bring Forward lay objects that are on the same layer gaf Sens Chal 2 a for inserting a text object Rectangle for inserting various graphic objects into the overlay _ Z Ellipse Line Arrow Highlighter for highlighting any rectangular image area in color The high lighted image segment looks like a color transparency has been placed over the image area Burning an overlay writes the overlay information into the image thus overwriting im age information The burning of an overlay is not necessary for any application within your image analysis program Burning an overlay is necessary e g when you wish to export an image along with its overlay into another application program such as MS Word This is the only way for
314. you find all the record objects currently defined in the current report template If the re port template only has one or no format at all for record objects the record object will automatically be inserted in a standard format gt The predefined standard record object only contains predefined fields which exist in every image database The content of these fields will be au tomatically included in the report 5 Now select several thumbnails in the database You do this by keeping the Ctrl key depressed and selecting the various images via leftclick 6 Drag the thumbnails from the database window directly on the first database ob is ject located on the report page Object templates 202 This is how to insert records from a database directly into a report se lect all database records you wish to include in the report Drag the im ages selected keeping the left mouse button depressed onto the first record object within the report window The records in the illustration have been selected as thumbnails Report Generator Record objects Step by step gt Ifthe number of records selected is greater than the number of record ob jects your image analysis program will automatically add the necessary number of pages gt Images are always added in the order in which they were selected in the database window amp LeamSIS apl 5 Ea h LeamS S_apl O i ih ji igi i agi ji rt See ee ee ee
315. your micro scope Only the objectives selected during installation are shown and offered in the Set Magnification dialog box and can be conveniently selected from a list Should your light microscope be remote controlled you do not have to provide any objective magnifications since the magnification is automatically selected e Should you decide to change your objective after software installation you can also provide a magnification during image acquisition which is not provided in the list The image is then correctly calibrated based on the automatic calibra tion data even if the magnification is not provided in the magnification list e lItis always possible to manually calibrate even a precalibrated input channel In doing so the predefined calibration data is overwritten To avoid this duplicate an input before altering the calibration data e Should you update an already existing software version Always select the Up date option during setup In this case already existing input channels will not be altered The precalibrated inputs will be additionally installed e Check a precalibrated input This makes sure that the end magnification of your system has been correctly calculated The calibration data of an existing image may be modified at a later point in time This will be necessary if you have acquired an image using a non calibrated input e g using a scanner In this case the XY calibration is automatically set to 1 Pixel

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