AIDA Image Analyzer Multi Labeling User's Guide
Contents
1. moving flipping and rotating From the MOVE drop down list select the image you want to move flip or rotate Move m 1 pools1 tif Then drag it with the mouse pointer to the desired position in the MULTI CHANNEL dx mm IMAGE window You may also use the 0 000 arrow keys on your keyboard to move the aeg 0 000 image by pixel Alternatively you can enter the shift values for x and or y direction in the appropriate combo boxes below the MOVE drop down list AP aL K Cancel E ES New Multi Channel Yiew Pools2 adf ES New Multi Channel Yiew Pools2 adf ejtjoje Use the first two of the four buttons to horizontally and vertically flip the image and the remaining two to rotate the image by 90 degrees counterclockwise and clockwise respectively no pixel interpolation necessary Accomplish the move action by clicking the OK button on the MOVE panel unless you confirm the action no previously computed value will be changed You can use the VIEW button to open the MULTI CHANNEL IMAGE window for displaying the overlaid images User s Guide AIDA Image Analyzer Multi Labeling Multi Channel Control Toolbox e 7 If you want to switch a channel temporally l off so that this channel is no longer shown m e Examples Pools2 ack in the MULTI CHANNEL IMAGE a e Examples Pools1 adf window select the appropriate colored check box next to the file path indicating the channel s image Enabling or disabling a ch2. of the COLORSCALE SCALES and WHITE BG see the respective description in the Publishing Layout Toolbox section above 10 e User Interface of Multi Labeling User s Guide AIDA Image Analyzer Multi Labeling Preview User s Guide AIDA Image Analyzer Multi Labeling As for printing in AIDA there are two ways of previewing pages before they are actually printed 1 Using the PRINT PREVIEW option of the FILE menu or 2 using the PREVIEW button on the PUBLISHING LAYOUT toolbox The PRINT PREVIEW option of the FILE menu opens the PREVIEW dialog box which allows you to specify the layout settings for the preview The options presented here are the same as in the PRINT dialog box and those selectable from the various sections of the PUBLISHING LAYOUT toolbox However they are not stored with the data file The PREVIEW option of the PUBLISHING LAYOUT toolbox allows you to preview all pages as configured in the PUBLISHING LAYOUT toolbox before they are actually printed Clicking the PREVIEW button opens the PREVIEW window directly since all layout setting are already made through the PRINT PROTOCOL panel Aida 1D Multi Labeling Preview Pools2 adf File Edit Evaluation Options View Window Help lt gt Close Page 1 of 5 Page 2 0f5 Preview e 11 Export Export Image To export the content of the MULTI CHANNEL IMAGE window in a raster graphic format choose the MULTI CHANNEL IMAGE option from the EXPOR
3. N toolbox being enabled then 10 Click the N button to normalize Report Ela elele Nis 11 Open the 2D REGION REPORT window see below You will see some columns which have the suffix Chan 2 attached These are the values for the corresponding region on the normalization channel 12 Further you will see some columns which have the suffix Norm attached These are the normalized values A normalized value is the value of a region on the master image divided by the value of the region on the normalization image Region Report pools2 adf No Grp Type Area Integral Int Norm Int Chan 2 Int Bkg Norm Integral Bkg Int Bkg Chan 2 oo Ine L OL aL aL g 98795 0 0 9 333220 98795 0 Sal I essen 12 563530 56353 0 3 o 55 69410 0 69410 0 E 8 ol osf nemno 1300140 oj 10 3509240 35485720 34 6 393322 0 0 1 User s Guide AIDA Image Analyzer Multi Labeling Performing 2D Multi Labeling Evaluations e 15
4. T submenu of the FILE menu or select the COPY CONTENT from the EDIT menu The MULTI CHANNEL EXPORT dialog box opens asking you to specify a name and data format Windows Bitmap or CompuServe GIF format for the image export file Multi Channel Export Pools2 adf ax Save in E Examples ff m E File name pools2 1 bmp I Save as type windows Bitmap y Cancel After you confirmed the export by clicking the SAVE button the MULTI CHANNEL EXPORT OPTIONS dialog box appears allowing you to set further option for the image file export Multi Channel Export Options x Bitmap Size Width 10 16cm Export Data OK Cancel Jl Depending on the purpose of the export bitmap you can select the size and resolution of the resulting bitmap The raster graphic 1s exported in the Windows Bitmap or the CompuServe GIF format 12 e User Interface of Multi Labeling User s Guide AIDA Image Analyzer Multi Labeling Performing Multi Labeling Evaluations Performing 1D Multi Labeling Evaluations With the 1D MULTI LABELING evaluation mode you can take over a runlength calibration from one image to another To take over a runlength calibration from the reference image second channel to the master image first channel follow these steps l 10 Open the image on which your standards for runlength calibration are visible Perform your runlength calibration here as usual and save it say under the name A ADF O
5. User s Guide AIDA Image Analyzer Multi Labeling raytest Isotopenme ger te GmbH AIDA Image Analyzer Multi Labeling User s Guide The software described in this manual is furnished under a license agreement and may be used only in accordance with the terms of the agreement Copyright Notice Copyright c 2001 raytest IsotopenmeBgerate GmbH All Rights Reserved This document may not in whole or in part be copied photocopied reproduced translated or reduced to any electronic medium or machine readable form without prior consent in writing from raytest Isotopenme ger te GmbH Benzstr 4 75334 Straubenhardt Germany Trademarks AIDA Image Analyzer AIDA Array Metrix AIDA Annotation AIDA 1D Multi Labeling AIDA 1D Evaluation AIDA 1D Densitometry AIDA 2D Multi Labeling AIDA 2D Densitometry AIDA Easy Array AIDA Whole Body Autoradiography AIDA 1D Thin Layer Chromatography AIDA 2D Thin Layer Chromatography are trademarks of raytest IsotopenmeBgerate GmbH Other product names mentioned in this manual may be trademarks or registered trademarks of their respective companies and are the sole property of their respective manufacturers 2001 05 1 0 Table of Contents Introduction 3 Sarina Mulltbabeline aussen a EEE 3 User Interface of Multi Labeling 5 Data Windowsin Multi Labels EI 5 Multi Channel Image Window sinimni einen a Ben E EHI 5 Multi hanne iControl Toolbar anna 6 Publishing Toolbox in Mu
6. annel does not change any computed values Transfer Curve Section The controls of TRANSFER CURVE section are used to adjust the contrast of the images in the MULTI CHANNEL Ms IMAGE window Select the channel to which the controls should be applied by selecting the appropriate colored button above the histogram window The histogram window and its controls below are similar to those of the DISPLAY CONTROL toolbox described in the AIDA Image Analyzer Basic Concepts and Features User s Guide Transfer Curve Quantum level led Range Y Quantum level gt Gamma 5 Curve Autome PSL Curve 8 e User Interface of Multi Labeling User s Guide AIDA Image Analyzer Multi Labeling User s Guide AIDA Image Analyzer Multi Labeling Publishing Toolbox in Multi Labeling In MULTI LABELING the PUBLISHING LAYOUT toolbox of the respective core evaluation module 1D EVALUATION or 2D DENSITOMETRY is expanded by an additional button for specifying the print options for the MULTI CHANNEL IMAGE window Bl Selecting the MULTI CHANNEL option you can specify the paper orientation for the printout as well as the items you want to print In the FORMAT part select the paper orientation for the printout PORTRAIT or LANDSCAPE The s ze of the image can be automatically adjusted to fit the page AUTOMATIC SIZE Alternatively you can enter the zoom factor in percent The PARAMETER checkbox of the PRINT controls section ena
7. bles the printing of the data and comment which are found in the FILE INFORMATION box Check WHITE BG if you want to set the background color for the printout to white instead of black default Selecting COLORSCALE prints a bar next to the image showing the representation of various signal intensities as color scale in the way it was set for the image SCALES prints a bar next to the image that shows the length representation in the image A Publishing Layout Annotate 21 Jalfojojo Protocol Print a Print Preview Fs Multi Channel Format Portrait C Landscape Automatic Size CHo 10 Print Y Parameter V Images White BG V Colorscale Y Scales Publishing Toolbox in Multi Labeling e 9 Print In AIDA there are two ways for printing your image and evaluation data 1 Select the PRINT option from the FILE menu or 2 usethe PROTOCOL PRINT section on the PUBLISHING LAYOUT toolbox The PRINT command of the FILE menu allows you to print your data on the fly without permanently storing the layout printing settings whereas the PROTOCOL PRINT panel provides you with a complete set of printing features which includes saving the setting with the data file for reasons of reproducibility Selecting the PRINT option from the FILE menu opens the PRINT dialog box allowing you to configure the printout to contain only the overlays results and graphs that are currently needed C
8. ded version of 2D DENSITOMETRY Using 1D MULTI LABELING you can transfer the runlength calibration for MW IF etc from one calibration image to the master image 2D MULTI LABELING allows you to normalize one master image using a second one The core component of the MULTI LABELING add on is constituted by the MULTI CHANNEL DISPLAY function responsible for visualizing the image comparison in 1D MULTI LABELING and 2D MULTI LABELING Change Evaluation Mode Available Evaluation Modes 10 Multi Labelinc 2D Multi Labeling Multi Channel Display Cancel Depending on the desired evaluation select the appropriate evaluation mode 1D MULTI LABELING 2D MULTI LABELING by clicking the EVALUATION button in the toolbar A dialog box appears offering you a list of available evaluation modes The list entries reflect the installed AIDA application modules Select the appropriate list item und click OK Note that these evaluation modes are only available if you purchased the AIDA MULTI LABELING option 4 e Introduction User s Guide AIDA Image Analyzer Multi Labeling User Interface of Multi Labeling Data Windows in Multi Labeling In addition to the AIDA standard data windows IMAGE and HISTOGRAM and the additional data windows specific to the respective core module the following data window is available in the MULTI LABELING mode e MULTI CHANNEL IMAGE You can access this data window by selecting the MULTI CHANNEL IMAGE entry fr
9. li Eabeling nu ann 9 Pille tb i etc I i be ie ac deb ee 10 PEN gts ti it tse loc fai ec fbr le ce sfc ect bra a Rtas a si pm IL 11 A A AAA 12 AN A NEUE IEUEUEHEHLRENEHENEEIR EEBEREEIEHEUE FERENEBENEUEREEEEEIEERSUERFER 12 Performing Multi Labeling Evaluations 13 Performing 1D Multi Labeling Evaluati0DS ooooccnnonoccccnononnnnnnonannnnnnononnncnnnnnnnnnnnnononnnnnnnnns 13 Performing 2D Multi Labeling Evaluati0DS oooocccnooococcnononannnnnononnnnnonnnnnnncnnnnn cnn conan nnnncnnnnos 15 Introduction Starting Multi Labeling The AIDA MULTI LABELING modules allow you to evaluate one image the master image by comparing it with one or two other images and to eas ly visualize the result of the comparison For this purpose the images can be displayed in lookup table colors red green or blue instead of grayscales superimposed on each other The combined colors resulting from this additive color synthesis indicate relative s gnal strength For example you can combine the scans of up to three different fluorescent dyes into a single image or you can compare re probed blots by using the same label AIDA MULTI LABELING is actually an add on for the 1D EVALUATION and 2D DENSITOMETRY module respectively supplementing MULTI CHANNEL DISPLAY functionality Therefore 1D MULTI LABELING represents the MULTI CHANNEL DISPLAY extended version of 1D EVALUATION whereas 2D MULTI LABELING can be described as the MULTI CHANNEL DISPLAY exten
10. lick the check boxes for the various items to enable or disable them Select the number of copies you want to print Print 2D Multi Labeling Pools1 adf x Printer EPSON EPL 5700L Advanced at LPT1 OK Cancel top 20m E fom y Header Printer z Parameter Parameter and Image Options Image whole image Y W overlays Multichannel Parameter portrait v grayscale Multichannel Image scales automatic s Region Report r foo overexposed Region Calibration Multichannel Print Options wholeimage 7 white bg portrait vw Y colorscale Y scales automatic size O 1100 a Region Report Options portrait In addition to the PARAMETER and IMAGE standard AIDA checkboxes and the checkboxes specific to the respective core evaluation module the MULTICHANNEL PARAMETER and MULTICHANNEL IMAGE checkboxes are available in the left part of the PRINT toolbox Select the appropriate checkboxes to include the respective information in the printout The MULTICHANNEL PRINT OPTIONS section allows you to set the printing options for the MULTI CHANNEL IMAGE printout As for the PARAMETER AND IMAGE OPTIONS section you can configure the content range of the printout WHOLE IMAGE or WINDOW CONTENT the paper orientation LANDSCAPE or PORTRAIT and the s ze of the image representation AUTOMATIC SIZE or relative size in Use the three check boxes on the right part of the section to enable or disable the printing
11. lti Labeling Performing 2D Multi Labeling Evaluations With the 2D MULTI LABELING evaluation mode you can use one image to normalize the region quantities of another related one To use a reference image second channel to normalize the region quantities of another image master image first channel follow these steps 1 Open the image which you want to be normalized say it is called B TIF 2 Select the MULTI CHANNEL CONTROL toolbox and click the SELECT button 3 Choose the image which you want to use to normalize the B TIF as normalization channel Say it is called A TIF 4 The MULTI CHANNEL IMAGE window appears Select the MOVE button from the MULTI CHANNEL CONTROL toolbox 5 Use the mouse to move the red channel so that it lies exactly over the green channel You may use the arrow keys on the keyboard to move the red channel in x and or y direction by pixel 6 Ifyou want to zoom during the move action use the PLUS or the MINUS key on the keyboard 7 You may want to use the ZOOM mode But since this mode cannot cooperate with the MOVE mode you have to click the MOVE button again after switching to ZOOM mode if you want to move the image further 8 When you are content with the congruence of the channels press OK in the MOVE dialog Now you can close the MULTI CHANNEL IMAGE window 9 Draw aregion on B TIF You will see the N button N for Normalization on the REPORT section of the REGION DETERMINATIO
12. m the MULTI CHANNEL IMAGE window as well as the colors for both images Edit Channels ET Measure Channel Red X Quantum level v e Examples Pools2 adf Standard Channel Channel 2 y ge EX y OK Cancel To select a image for the reference channel called STANDARD CHANNEL or NORMALIZATION CHANNEL depending on the active MULTI Ki F LABELING mode click the BROWSE button The OPEN FILE dialog box appears prompting you to choose a file You can select pure images like TIFF or BMP files or AIDA Evaluation files adf Since each ADF file is associated to exactly one image by selecting an ADF file you actually select the image associated with To remove an image from the reference channel just delete its name in the combo box Note that in 2D MULTI LABELING the image of the second channel automatically becomes the normalizing image 6 e User Interface of Multi Labeling User s Guide AIDA Image Analyzer Multi Labeling In ID MULTI LABELING you will be asked whether the runlength calibration should be taken over from the added channel to the master image Of course the runlength calibration can only be taken over from the added channel if you have made a runlength calibration on that image at all Use the MOVE button to move and or rotate the images against each other If you click the button the top section of the MULTI CHANNEL CONTROL toolbox is changed providing controls for
13. om the VIEW menu Multi Channel Image Window In the MULTI CHANNEL IMAGE window the overlaid images are displayed After selecting a master image and one or two reference images using the controls of the MULTI CHANNEL CONTROL toolbox see below you can adjust the position of these images to yield maximum superimposition ES New Multi Channel iew Pools2 adf Multi Channel Control Toolbox ml In addition to the standard AIDA toolboxes DISPLAY CONTROL and PUBLISHING LAYOUT and the core evaluation module specific toolboxes the MULTI CHANNEL CONTROL toolbox becomes available after selecting the appropriate MULTI LABELING evaluation mode You can access these additional toolboxes from the EVALUATION menu or by clicking the appropriate button on the toolbar The controls of the MULTI CHANNEL F Multi Channel Control CONTROL toolbox allow you to add images to the master image to move them against each other and to adjust the Select Move View contrast of the images in the MULTI CHANNEL IMAGE window To display the MULTI CHANNEL m e 4 Examples Pools2 adf CONTROL toolbox a e Examples Pools1 adf On the main menu click EVALUATION and then click MULTI CHANNEL CONTROL Alternatively you can select Transfer Curve the MULTI CHANNEL CONTROL button on the toolbar zz Clicking the SELECT button opens the EDIT CHANNELS dialog box which is used to select a reference image to be added to or removed fro
14. pen the master image on which the standards are not visible Say this s called B TIF Select the MULTI CHANNEL CONTROL toolbox and click the SELECT button Choose A ADF as second channel It is important that you choose the ADF file and not only an image file like A TIF This is because the runlength calibrations are always stored in the ADF files never in image files Click OK Now you are asked if you want to take over the runlength calibration from A ADF Click OK The MULTI CHANNEL IMAGE window appears Select the MOVE button from the MULTI CHANNEL CONTROL toolbox Use the mouse to move the red channel so that it lies exactly over the green channel You may use the arrow keys on the keyboard to move the red channel by pixel e If you want to zoom during the move action use the PLUS or the MINUS key on the keyboard e You may want to use the ZOOM mode But since this mode cannot cooperate with the MOVE mode you have to click the MOVE button again after using the ZOOM button if you want to move the image further When you are content with the congruence of the channels click OK in the MOVE dialog Now you can close the MULTI CHANNEL IMAGE window 11 The calibration lines are now transferred into the B TIF If you draw a profile with peaks in B TIF their runlengths are calibrated using the calibration taken over from A ADF 14 e Performing Multi Labeling Evaluations User s Guide AIDA Image Analyzer Mu
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