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CTan User Manual - University of Manitoba

1. COPY Copies one dataset onto another for instance ROI COPY image will make the ROI become an exact copy of the currently loaded image Note this operation replaces the previous function image copy that in earlier CTAn versions was listed under the shrink wrap function NOT This operation selects the part of the image that is not in the selected original dataset i e either not in the image or not in the ROI OR This operation selects the part of the image that is either in the original image or in the ROI including parts that are in both AND This function causes the resultant image to correspond to only the parts or pixels of the image that are the same in both the image dataset and the ROI An example of this is the useful function image image AND ROI which has the effect of removing all parts of the image outside the ROI providing the ROI is a binary mask XOR This function selects the part of the image that is either in the original image or in the ROI but excluding any part that was in both the original image and the ROI SUB Subtracts one image from the other SWAP Swaps image and ROI image becomes ROI ROI becomes image Page 103 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The following table depicts graphically the logical Boolean image operations carried out by functions within the BITWISE plug in BITWISE Image before ROI before Image after ROI after function BITW
2. Page 38 of 112 Manual for SkyScan CT Analyser v 1 10 7 4 3 Path measurement with the manual measure tool With this tab selected left mouse button drag and drop measures the length of a freehand path in the chosen unit Measure tool Angle Line m Path Coordinate path 2 091 mm path 2 343 mm aot path 2 116 mm path 2 735 mm Clear aT path 0 161 mm SS Length 2 051 mm path 2 487 mm Save path 2 473 mm path 0 896 mm path 0 911 mm 7 4 4 Coordinate measurement with the manual measure tool With this fourth tab selected left mouse clicks record the XYZ coordinates of the clicked point gt gt Ele amp Measure tool a Raw images Angle Line Path Coordinate x 2 1 0024E 001 6 3375E 000 4 1984E 000 mm A Autofill y 2 6 0061E 000 5 1363E 000 4 1984E 000 mm m wy 1 4498E 001 5 8611E 000 4 1984E 000 mm yz 5 3641E 000 2 1746E 000 4 1984E 000 mm x y 2 1 2447E 001 1 6983E 000 4 1984E 000 mm Clear Save o gt Page 39 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Measure tool function buttons e Autofill On completion of each mouse operation the measurement of the marked item will be automatically added to the displayed data list e Clear The displayed list of measurements will be cleared e Save By clicking on the save button all currently displayed m
3. _ Advanced l Brief description of the preference tabs e The general tab This contains options for the output of measured 3d and 2d parameters nomenclature unit notation and the text report file extension Other options support the import of different image formats setting the JPG compression level and an option for a tool tip showing XY image position e Animation This tab allows you to adjust the speed of animation both for display visualisation and for exported avi movie files e Region of interest This includes default options square or round for the region of interest ROI and size options for saving ROI datasets Options for loading ROI roi files are also given see chapter 8 e Histogram This tab is used to apply calibration to bone mineral density BMD Note that other non bone density scales could also be calibrated using this function just rename the density result accordingly chapter 9 e Volume This tab has options concerning the resolution level of real time volume modeling in CTAn which are constrained by the computer s video graphics card see chapter 6 e Tools In this tab you enter the directory path to the SkyScan CTVol program to allow it to automatically open on creation of a 3D model file e Directories In this tab you can specify the directory path to a temporary file required by CTA
4. 2010 When 3d output is selected the option to append summary results to a line by line text report file becomes available Individual object analysis This plug in runs an analysis of the morphometric parameters of individual objects in 2d or 3d Discreet objects are defined in either 2d or 3d as being completely surrounded by black space pixels This plug in implements the corresponding 2d and 3d individual object analyses in the 4 processed images page of CTAn as described in section 9 1 1 In the case that 3d space i e analyse individual objects in 3d is selected then a tick box option appears for saving the results which can be quite voluminous to a separate text file this option is recommended Separate file Bitwise operations Bitwise operations allow a number of Boolean or logical operations to be applied between the current loaded dataset which we can call the image dataset and the current ROI For the purpose of the Bitwise functions it is best to consider the ROI as a parallel dataset Note that both the image dataset and the ROI can be either binary or grayscale images The operations available under the Bitwise module are as shown in the image below COPY NOT OR AND XOR SUB and SWAP Page 102 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Bitwise operations aai Image 7 Image a or aaar Region of Interest a COPY Se Cancel AND XOR SUB SWAP
5. Background colour indicates what colour black or white will fill in areas of the new resliced images outside the boundaries of the initial images Using Slice spacing you can set the distance between cuts and Number of slices indicates the total number of slices in a resliced dataset 3 S gt 5 f y re s lt te A Tap i D A ON j AF r Gig Ra N Ya os a a i E O9 Tq Kien p ay 4 4 SET YS z pre 4 SAE TSO R M CP ae F I Mh MN AA JMJ tij SLRLSIESEIETENIETEE Reslice model Background color D 5 OK Slice spacing 1 Cancel Number of slices 1200 from 1581 Page 33 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Simultaneously with modifying these parameters the area selected for longitudinal resampling changes in real time in the crossection image window The areas outside of this selection are inverted On pressing the button the process of reslicing begins and after completion a dialog appears displaying the new resliced set of images You can view through the resliced images by moving the slider at the bottom of the dialog A line drawn in the resampling region in the crossection image corresponds to the current position selected by the slider You can save the single currently displayed resliced image in the dialog by r pressing the button Save image A new dataset of all the resliced images can be saved with a new prefix by pressing
6. Fit to Window Actual Size Animation Hand mode b Fv EWP P 4 d Properties Note that while the results window is open for individual object 2d analysis the highlighted object is shown with a small target mark on the image as indicated by arrows on the image above Page 63 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Choose Details Select the details you want to display for the results Details Area mm 2 Perimeter mrm Form factor Euler number Porosity 4 Extent Orientation Eccentricity Centroid x mm Centroid y mmm Moments of inertia x mm4 Moments of inertia y mm 4 Width of selected column in pixels Restore Default You can save the results of individual analysis of image objects as a text file by E pressing the button Save results You have the option to select which 2d parameters are included as columns by clicking on the Choose details button A iq dialog will open as shown below Then you can print them by pressing the button Print results Pressing the button Close window will close the dialog window 10 4 Individual object analysis in 3d This analysis calculates and reports the 3d parameters of each and every discreet 3d binarised object within the VOI Note that unlike with the integrated 3d objet analysis on clicking the button to start individual 3d analysis no window will open to prompt for output filenames etc instead the calculatio
7. Number of objects Obi 38 dle Save histogram of distribution Total RO area Tar 12 6059 mim 2 Object area Oby Ar 2 91763 ror Percent object area Obj Ar T Ar 23 14490 W123 Show absolute values Total ROI perimeter T Fm 14 19776 mm i Object perimeter Obj Pm 195 28175 mm F Object perimeter area ratio Obj Pm ObiAr 66 93173 17mm iia ize distribution Average object area Av ObjAr 0 00502 min 2 Length distribution Average object size Ay Ob Le 0 07996 mm s0 Perimeter distribution Fragmentation index Fr 22 94119 1mm ee eee Euler number Eu H 415 Fercent porosity Fo 0 53704 a i Orientation distribution Centroid Crd 0 41363 mm Porosity distribution Centroid y Crd 0 01598 mm Moment of inertia ha MAL 2 1 64933 mm4 Moment of inertia y ha bal 2 2299 mm4 Polar Moment of inertia MM polar 3 07924 rn 4 Product of inertia Prin 0 1 2326 mm4 f 4 Individual 2D object analysts 10 3 Individual object analysis in 2d You can select any item in the single image 2d data report by left mouse click and a small flashing cross inside a circle will appear on the crossection image indicating the centroid of the selected item see figure to the right Furthermore within the same image field if you right click on any discreet binarised object a drop menu will appear with the top item being object properties figure below lower Selecting object properties will open a 2d results box wi
8. The histogram table has five columns which display 1 the absolute values of image brightness 2 the relative brightness as a 3 the absolute value of the image Page 50 of 112 Manual for SkyScan CT Analyser v 1 10 2010 area with this brightness shown in current units of measurement 4 the area with a specific brightness as a of the total area with all brightness values and 5 the area with a specific brightness as a of the total area with brightness within the selected range Note that at the top of the histogram table there are four tabs with alternative units of brightness or density These are grayscale Hounsfield units HU bone mineral density BMD and attenuation coefficient How these three are inter calibrated will be described below At the bottom of the table the mean brightness value from the whole histogram is shown mean total Further data from the brightness histogram are given the boundaries of the binary selection the total number of dataset voxels within the binary selection the mean brightness within the binary threshold selection and the standard deviation standard error of mean and the 95 confidence limits relating to the brightness mean value within the threshold limits Eee Grayscale indexes Index 2 Area mm 2 Total Selected 250 98 0 0 00000 0 000 0 000 251 98 4 0 00000 0 000 0 000 252 98 8 0 00000 0 000 0 000 253 S9 2 0 00000 0 000 0 000 254 99 6
9. snail_rec0276 bmp Both left and right mouse button drag and drop are used to control the models position e Left mouse button drag and drop rotates the model e Right mouse button drag and drop movement controls near and far movement movement toward the volume screen center moves the model away movement away from the center moves the model closer Page 28 of 112 Manual for SkyScan CT Analyser v 1 10 2010 6 2 1 The volume modeling buttons from right to left fi save the currently displayed image what you see is what you get Build a volume model of the complete currently open dataset Build a volume model from the volume of interest within the currently open dataset ie Reset the model position to the starting position T Place a visible clip box around the model panes of the clip box facing the user can be moved relative to the model by shift left mouse button drag and drop to cut away and expose surfaces within the model The clip box and model together can be rotated by left mouse button drag and drop The clip box alone can be rotated model remains stationary by left mouse button drag and drop with control key held down O Place a clipping plane next to the model which can be moved relative to the model by shift left mouse button drag and drop to cut away and expose surfaces within the model The clip plane and model together can be rotated by left mouse button drag and drop The clip plane
10. 0 00000 0 000 0 000 255 100 0 0 00000 0 000 0 000 Mean total 15 039 seseeesee Selection 2 Begin 85 End 255 Number of voxels 53403 Mean 155 310 Help Standard deviation 29 560 Standard error of mea 0 128 Se Save Histogram 95 confidence limits Minimum 155 055 Maximum 155 566 Ro ate Logarithm scale f Calibration In the histogram window and table the current binary oe aes selection is highlighted by white colour with non selected From Selection parts shown highlighted in light brown To change the 3 From Dataset boundaries of this selection use the two sliders located i Grayscale Indexes above and below the histogram window To the left of E i this window is a vertical slider for histogram scaling pote edhan Bone Mineral Density You can use the buttons and tabs of the Histogram bar to access commands located in the Histogram menu You can also open this menu by pressing the right PE Halftone view mouse button anywhere in the histogram window v ROlview Attenuation Coefficients Page 51 of 112 Manual for SkyScan CT Analyser v 1 10 2010 9 1 1 Commands of the Histogram menu Histogram Save Histogram saves in a text file prefix_hist txt the values ES of the histogram table displayed at the given moment Histogram Save Auto threshold automatically assigns a threshold KE selection Histogram Logarithm scale switches the histogram display mode A bet
11. 16 2010 6 11 PM 2 16 2010 6 11 PM 2AA IN1N 6 11 DM Type Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Bitmap Image Ritman Imane _ Resize by n File name Files of type Ai SUDDOnNed Ties 27ND 0a TA All supported files bmp jpg tif raw BMP files bmp JPEG files jpg TIFF files ti Raw data raw _ Open as In the box after Raw data file type in the Preferences dialog you should enter the extension of non SkyScan file format The raw data file RDF can be a single volume or a multiple volume if files have a suffix with four digits For a multiple volume RDF the information about Z position is taken from suffix 4 digit number Page 14 of 112 Manual for SkyScan CT Analyser v 1 10 2010 On loading a non SkyScan dataset the user must specify the type of data under the following headings corresponding to boxes in the import raw data dialog box shown above e Data type integer floating point etc e Byte order little endian WIN big endian MAC see the Wikipedia entry http en wikipedia org wiki Endianness e Header size in bytes e Pixel size in microns e Image width and height pixels e Major and minor value these are the minimum and maximum grey level By default these are assumed as 0 and 255 for 8 bit format For datasets with different grey level bit depth the mini
12. 25 and 0 75 g cm Density range calibration Calibration unit Min value Max value BMD 2 0 75 Attenuation 0 0281 Page 54 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Please note that on pressing OK after entering calibration values a permanent calibration is established which is written to your computer s registry This calibration will remain in place after restart of the computer 9 3 Modes of image view at the binary page The toggle halftone view and toggle ROI view buttons are respectively at the right end of the button bar above the density histogram at the histogram page Histogram The four image modes shown below are selectable by switching the options for halftone binary image view and ROl full image view 9 4 File menu items at the histogram page File Save Binary saves the dataset as binary images with the current f threshold in 1 bit bmp format small file size File Create 3D model creates a file of a three dimensional model for viewing in the program CTvol exe You can select the model file type Sa The 3D model created in CTAn can be saved as three file types i a ctm file which saves a model with a spatial measurement unit of voxels il a p3g file type which also has a spatial unit of voxels and saves a given model with a much smaller file size which also opens quicker in CTVol although file creation in CTAn can be Page 55 of 112 Manual f
13. algorithm If you choose Adaptive Rendering configuration boxes will appear in which you should specify the locality and tolerance variable parameters Directories Advanced 3D suface construction algonthm MIL line spacing Fed puels 7 Locality 10 Tolerance 0 25 Page 57 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The Locality and tolerance parameters for adaptive rendered 3D models e Locality this parameter defines the distance in pixels to the neighboring point used for finding the object border Increasing this value allows jumping through noise on the object border but small objects often created by binarisation of noise with size less than this parameter will be lost e Tolerance this parameter defines the sub pixel accuracy with which the object border is delineated Reducing this number makes the model more smooth and accurate but increases the model file size lt is possible to display or hide the Histogram bar from the menu inn View Histogram Page 58 of 112 Manual for SkyScan CT Analyser v 1 10 2010 10 Page 4 Morphometry The morphometry calculation page the 4 page is where 3d and 2d measurements are made and it becomes accessible only after the dataset grey scale images are transformed to binary at the binary 3 page The areas painted white in the binary page are identified as solid objects and all that is painted black is considered ambient background On m
14. alone can be rotated model remains stationary by left mouse button drag and drop with control key held down Toggle navigation clip plane clip plane within a cube bounding the model Toggle XYZ 3D direction key View the model in volume rendered model mode 3A ATN View the model as an attenuation map MIP View the model as a maximum intensity projection Page 29 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The three model viewing modes of OVR volume model ATN attenuation image and MIP maximum intensity projection shown left to right for a snail shell The ATN image has false colour applied A clip box can be applied to a displayed model Holding down the keyboard shift button and then making a left button drag and drop allows any clip box pane facing the user to be selected in red and moved to make a cut through the model in real time A clip plane can be used in a similar way as the clip box above Page 30 of 112 Manual for SkyScan CT Analyser v 1 10 2010 7 Page 1 Raw Images This first page raw images is where you find yourself first after opening a dataset in CTAn In this page you can view the dataset in a number of different ways in preparation to moving on to the further analysis related pages 2 5 There are a few useful functions at the raw image page that it is worth being aware of After the five page buttons at the top left of the CTAn window there are a fu
15. and saves the currently loaded dataset list in the ctl format At the bottom of the BATMAN window from the left the following functions are present Start The start button starts batch processing of the list of datasets by the sequence of operations set out in the Task list Information about the progress of analysis is displayed in the Status column in both the upper task window and the lower dataset window Overwrite output files Selecting this option will result in any previous results of BATMAN calculations in any of the listed datasets in the default format prefix batman txt and prefix batman log being overwritten by the results of the present analysis Tum Off Computer at end of processing selecting this option will cause the computer to be fully shut down at the end of the operation of the task list This can be useful if you are launching a batch calculation on multiple datasets that will run overnight or over a weekend for example Close The close button closes the BATMAN window and stops batch processing if it is in progress Page 79 of 112 Manual for SkyScan CT Analyser v 1 10 2010 When a batch task list is in progress a progress bar will appear at the bottom of the window The Task List has three columns relating to each selected task Name the name of the internal or external plug in Description a description of the task performed by the plug in Status the st
16. boundary of a binarsed object iJ Reload Reload images or ROI iJ Histogram Image histogram I Individual object analysis Calculate individual parameters of objects J Bitwise operations Uperations based on binary arithmetic At the custom processing page there are two tabs containing lists of analysis or image processing functions referred to here as plug ins These are titled internal and external plug ins Internal plug ins are always available in CTAn The external plug ins tab can be populated by a users own software coded analysis function communication with SkyScan will allow the user s software routine to be formatted as a dll file and installed so as to be available in CTAn under the external plug ins tab This manual will describe only the internal plug ins Please note some plug ins only work on binary images such as despeckle and morphological operations These have to be placed after threshold in the order of tasks Otherwise you will get an error message image input must be black white Threshold Type Thresholding This plug in is where you set the two lower and upper thresholds for binarisation Global Background Radius Constant Under type there is a choice of global or adaptive Global is the simplest to apply and FTE pIOcasIDI applicable to most micro CT images If you A ii noe select adaptive you need to choose Type Levels Default levels Low Global v Global Ada
17. button is pressed 7 4 The hand measurement tool CT analyser provides a tool for manual measurement of angles straight line distances and distances along a free hand drawn non straight line The measurements are made on both the projection and crossection images The tool dialog is opened with the yellow protractor icon in the CTAn top button row B aan r Page 37 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The measure dialog has four tabs angle line path and coordinate Selecting one of these enables on screen measurement using left mouse click or drag and drop 7 4 1 Angle measurement with the manual measure tool Left button drag and drop enacts a protractor angle measurement relative to the horizontal plane Note however that pressing control after delineation of an angle then resuming mouse cursor movement will make the angle plane first drawn become the new reference plane in place of the default horizontal plane Angle Line Path Coordinate angle 127 55 angle 345 96 angle 340 08 angle 46 65 angle 236 34 7 4 2 Line measurement with the manual measure tool With this tab selected left mouse button drag and drop measures the length of the drawn straight line in the selected unit Measure tool Angle Line Path Coordinate line 0 912 mm line 0 353 mm line 0 740 mm line 0 484 mm line 0 424 mm
18. ec0289 bmp 289 line 12 154 mm ec0288 bmp 288 line 12 112 mm ile name snail snail__ snail snail__rec0287 bmp 287 line 12 069 mm snail__rec0286 bmp 286 line 12 027 mm snail__rec0285 bmp 285 line 11 985 mm snail__rec0284 bmp 284 line 11 943 mm snail__rec0283 bmp 283 line 11 901 mm snail__rec0282 bmp 282 line 11 859 mm snail__rec0281 bmp 281 line 11 817 mm snail__rec0280 bmp 280 line 11 775 mm snail_rec0279 bmp 279 line 11 733 mm IN snail__rec0278 bmp 278 line 11 691 mm E snail__rec0277 bmp 277 line 11 649 mm snail__rec0276 bmp 276 line 11 607 mm snail_rec0275 bmp 275 line 11 565 mm snail__rec0274 bmp 274 line 11 523 mm snail_rec0273 bmp 273 line 11 481 mm snail__rec0272 bmp 272 line 11 439 mm snail_rec0271 bmp 271 line 11 397 mm snail_rec0270 bmp 270 line 11 355 mm snail_rec0269 bmp 269 line 11 313 mm snail__rec0268 bmp 268 line 11 270 mm snail_rec0267 bmp 267 line 11 228 mm snail__rec0266 bmp 266 line 11 186 mm c snail_rec0265 bmp 265 line 11 144 mm E snail__rec0264 bmp 264 line 11 102 mm 4 snail_rec0263 bmp 263 line 11 060 mm 2 snail__rec0262 bmp 262 line 11 018 mm 3 PA snail rann hran DEA lina INAFE mrd T 5 z 4 w Histogram nat aA Blo From image From selection From dataset 255 c 74 ey a rayscale indexes Attenuation coefficient Bone mineral density G Palette Original x Q 90 Se 413 413 S
19. indicate the folder containing the external plug ins ctp and press the button OK These modifications will take effect only after a new loading of images Note that installation of the external plug ins is separate from the installation of C TAn itself When you switch to this custom processing mode a duplicate of the initial dataset is created and a progress bar will indicate this process Note to speed up operation in custom processing it helps to reduce dataset size by creating an ROI dataset Modifications to the dataset made in this mode are displayed in an image window and a new Plug Ins bar appears 11 1 Plug Ins bar The Plug Ins bar has the following tabs Task list shows the list of operations which can include internal and or external plug ins which will be applied to the dataset in the displayed order top down Internal shows the list of internal plug ins Page 74 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Plug Ine da ie 5 El Task list F intemal extemal igh Gutput Report Name Description 4 Thresholding Segment the foreground from background to binary images I Save bitmaps Save images to new folder 20 analysis Calculate 2D parameters of binary images f 3D analysis Calculate 30 parameters of binary images 2 Smoothing Smooth mages and remove a noi
20. of the open dataset pie Region of interest Reset All resets the region of interest of all E images to interpolated i e default This action can be considered as the start again button Region of interest Invert ROI this switches the selected active o ROI region from the region inside the selected shape to the region outside the selected shape and vice versa Region of interest Edited above switches to the next edited Ctrl f region of interest located above the current image Region of interest Edited below switches to the next fixed region Ctrl of interest located above the current image Region of interest Last Modified switches to the image containing region of interest last subject to modifications Region of interest Build Cube creates a cubic volume of interest VOI based on a square region of interest with the current image taken as the equatorial level of this cube The regions of interest for images outside of this cube will be set to empty regions of interest The equatorial level is indicated as a square ROI while all other levels are shown as rectangular ROIs Region of interest Build Sphere creates a sphere volume of interest based on a round region of interest with the current image taken as the equatorial level of this sphere The regions of interest for images outside of this sphere will be set to empty regions of interest The equatorial level is indicated as a round ROI
21. or higher and place the ant exe file in the same directory as ctan exe and the license file ctan lic In the history of develooment of CTAn there have been two upgrades which required re authentication of the CTAn license This involves re entry of your user name institute and ID number Please note that this does not require a new license only to remember where your license and license information are stored These are the upgrades in question 1 Upgrading from version 1 4 0 1 to 1 4 1 0 newer versions required re authentication of the CTAn license This upgrade was in early 2004 2 Updating from 1 6 1 1 to 1 6 1 2 involved two big changes 1 compatibility with VISTA and 2 the first compilation of parallel 32 bit and 64 bit versions for both Vista and XP This upgrade followed shortly after the first commercial release of the official rather than beta version of Microsoft Windows Vista This upgrade to 1 6 1 2 also required re authentication of the CTAn license Page 6 of 112 Manual for SkyScan CT Analyser v 1 10 2010 3 Set up of preferences To change program parameters to set default options and to precisely adjust CTAn for your purposes open the dialog Preferences which is always accessible from the menu File Preferences It has several tab pages with various settings and options which we will examine below as required in regard to different parts of the program Tools E Directories
22. saltatory reconstruction is selected every two or more slices Crossection images are produced by the SkyScan reconstruction program and can be written in 8 bit bmp 8 bit jog or 16 bit tiff format Page 109 of 112 Manual for SkyScan CT Analyser v 1 10 2010 CTAn CTVol Dataset Dialog box Drag and drop Feldkamp Instance Left click Live flag Micro CT NOT Page 110 of 112 The CT analyser program for dataset viewing analysis and 3D model building The CT volume program for viewing and manipulating 3D models and making animated movies A stack of crossection images made by cone beam reconstruction constituting the 3d image of the scanned object Files can be in bmp tiff or jog format A box opened onscreen by a mouse click or key stroke which is interactive allowing or requiring the user to enter selections or information To draw a line or move an object left click on an image pane at a starting position and with the left button held down move the cursor the appropriate end position At the end position release the left mouse button The algorithm developed by Feldkamp Feldkamp et al 1984 by which a 3D image dataset is reconstructed from a set of shadow projection images taken at different angular positions lf any program such as CTAn is opened several times concurrently on your pc with different files or datasets open in each case then each running session of the same progr
23. the button Save resliced images os You can display or hide the Profile bar from the menu View Profile m Maximum intensity projection MIP generates an MIP image in the selected Sp orientation Apply ROI allows you to draw or select an ROI shape in the ROI page then amp restrict the MIP image to the ROI area only 7 2 The maximum intensity projection MIP The MIP function is activated by starting the profile line In each column of voxels orthogonal to the selected plane the highest density value found is assigned to that position in the generated image MIP images can visualise dense structures surrounded by lower density medium Projection view horizontal j Background color E Cancel n Depth of projection 6 T es Number of projections 1 Page 34 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Projection wiew Background color Depth of projection Number of projections MIP options e Projection view There are two options for the direction of the generation of the MIP image These are 1 horizontal meaning in the z axis or 2 along profile meaning orthogonally across the direction of the currently drawn profile line e Background colour Here colour means black or white If the background colour is set to the same colour as the ambient background then the image generated will be the maximum intensity projection showing the denses
24. the projection image and the active crossection image To do this press the left mouse button inside the image and holding the button down shift the cursor to a new position From the initial position a line will be drawn and under the cursor a tool tip will appear with the length of this line After release of the button the drawn line and tool tip will disappear It is possible to display or hide the Shadow projection bar from the z menu View Shadow projection E Page 21 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Image Origin Text file type Frofile line s On the General tab in the dialog File Preferences you can make the following preference selections Nomenclature You can choose between two sets of names and symbols for the 2D and 3D parameters These are Bone ASBMR and General Scientific nomenclatures Unit You can select the unit in which the dimensional bars and rulers will be displayed and which will be applied to 2D and 3D measurements The options are microns millimeters inches or pixels Notation Select between scientific notation giving numbers with four decimal places in the format 1 2345 E 001 to give uniform precision level for numbers of all magnitude or standard number format with five decimal places e g 0 12345 Image Origin You can set the origin 0 0 XY position of the image coordinates to the left hand lower corner or the center Page 22 o
25. while all other levels are shown as elliptic ROIs Region of interest Load loads an ROI saved on the disk Fe e The information about the selected grey level thresholds in the binary page and also the vertical boundaries of the dataset volume of interest VOI is stored in the region of interest file ro On loading an ROI file it is Page 43 of 112 Manual for SkyScan CT Analyser v 1 10 2010 possible to automatically recover one or both of these selections To do this go to the dialog File Preferences and the tab Region of interest and under Load options click the box for Restore binary selection and or Restore view of interest Preferences Load options Restore binary selection Restore view of interest Save images O Full area Inside accumulated ROI bounds Prompt on load If you tick the box Prompt on load then on loading an ROI roi file to a dataset a dialog will open with tick boxes giving two options Load RO Restore view of interest EIEI v Restore binary selection Restore view of interest implies the vertical ROI selection upper and lower image bounds The binary threshold current at the time the ro file was saved can also be restored by activating Restore binary selection Under Save images the option to accumulated ROI bounds should normally be selected this allows created ROI datasets see below to be cropped down
26. 40 35698 Total VOI surface Ts 3 60232 mmA 2 Object surface ob 5 14 54102 mmA2 Intersection surface 1 5 1 34800 mm42 Object surface volume ratio Obj 5 0bj V 65 52247 1 mm Object surface density Obj 5 TV 26 44289 1 mm Fragmentation index Fr 1I 4 06507 1 mm centroid x crd x 0 09000 mm centroid y Crd v 0 00406 mm centroid z Crd 7 1 23391 mm Structure model index 5M1I 2 33050 Structure thickness 5t Th 0 09574 mm Structure linear density 5t Li 0n 4 21545 1 mm structure separation st sp 0 08803 mm Degree of anisotropy DA 1 42218 0 29685 Eigenvalue 1 202 03107 Eigenvalue 2 247 49493 Eigenvalue 3 287 32409 Fractal dimension FD 2 20905 Number of objects Obj N 212 Number of pores Po N 56 Volume of pores Po V 0 00051 mm 3 Percent porasity Po 0 22802 Structure thickness distribution st Th mm mm mn 3 74 0 004 0 011 0 00 7 0 00037 0 1 0 011 lt 0 078 0 014 0 002272 1 035 0 018 lt 0 025 0 021 0 00536 2 50 30 025 lt 0 032 0 028 0 00848 3 96 10 5 1 IMPORTANT NOTE 3D THICKNESS CALCULATION AND ROI INTERPOLATION Concerning thickness measurement in 3d from CTAn version 1 5 1 9 the thickness measurement sphere fitting algorithm in 3D has been updated To eliminate artefactual errors caused by virtual spheres going into the corners formed at the VOI boundary the 3d thickness analysis is carried out for the whole loaded dataset but the valu
27. 93 bmp 483 line 2 599 mm Wi 1_plaBbOk_disc_0482 bmp 482 line 2 593 mm 481 line 2 588 mm es x 1e 2 583 mm 4 T Selection Reference Ctrl Insert ve 2 577 mml _ Set the Top of Selection Ctrl Home e 2 572 mm 3 Set the Bottom of Selection Ctrl End 2 566 mm l z e 2 567 mm Selection a 2 eeen i 2 556 mm gt Animation Space 2 950 mm l e 2 545 mm T Lich Properties Alt Enter pe 2 5339 mm a SE nnn tne 2 534 mim plabOk_ disc 0470 bmp 470 line 2 529 mm Right clicking in the list box on a particular crossection image number causes a drop menu to appear which offers the following functions Selection Reference Ctr Insert This function sets the selected image level as a reference level for automatically setting the top and bottom of the selected VOI range Refer to 6 1 below for a detailed description of the reference level function lace he ia Ctrl Home Clicking on this option sets the current image level as the top of the selected VOI range Set the Bottom of Selection Ctri End Clicking on this option sets the current image level as the bottom of the selected VOI range fs Selection Clicking on this option opens the selection dialog box for either direct entry of upper and lower range limit or the analytic box for use of preset offset and VOI height eae aaa Ese Starts and stops animation through the crossections within the selected VOI range L
28. 96 mm Height 1400 piele 4 546 mm position 953 line 3 095 mrm You can change the magnification of the displayed crossection image i e Zoom in and out by holding down the shift button and moving the mouse wheel After zooming in you can move to a selected part of the image using the scroll bars on the lefty and lower borders of the image window Note that any image magnification and position selected in one image page such as raw image viewing will be reproduced exactly if you move to the other viewing pages such as ROI binary and processed images as shown in the images below S a4 i 7 E E A ke There is a hand icon button at the right of the upper menu bar Pressing this makes a hand icon appear in the crossection image which can be used for moving the image position by left mouse drag and drop It will move the image only where the magnification is such that the full image borders are outside the crossection image viewing window Pressing the hand button a second time makes it disappear and restores the default arrow cursor Page 18 of 112 Manual for SkyScan CT Analyser v 1 10 2010 4 3 Dataset bar For switching between crossection images there is the Dataset bar on which a list of the loaded dataset image files is displayed For moving up and down the list you can use the keys t or the slider located to the left of the dataset bar I ie Raw images File name position i 1_plaBbOk_disc_04
29. Amest Properties C Results AYC_fibulaSAy Amst C Results AYO_fibulaSAy Amst Report Import amp amp amp amp amp amp amp amp amp k Export 4 Oversrite output files Turn Off Computer at end of processing In the lower dialog window there is the list of datasets to be processed and to the Page 78 of 112 Manual for SkyScan CT Analyser v 1 10 2010 right of this window some buttons for customizing the list and controlling the batch processing adds a dataset to the list In the opened dialog any image from a dataset can be selected removes the highlighted dataset from the list indicates the region of interest ro file that will be opened when processing the corresponding dataset When this file is opened it will apply the grey scale binary thresholds and the vertical boundaries of the dataset volume of interest or not as defined in the settings of File Preferences Region of interest opens the analysis results file for a chosen dataset This file has the same prefix as the dataset images followed by the double extension batman txt opens the report log file for a chosen dataset This file has the same prefix as the dataset images followed by the double extension batman log opens a dialog with information about the dataset ROI and the location of the result and report files Imports a previously saved dataset list in the ctl format Exports
30. ISE BITWISE BITWISE BITWISE Image inside ROI after BITWISE operation Hone DOGG moo E e OE Ca E Ee 0E casa operation operation operation operation No BITWISE operation starting situation image COPY ROI ROI COPY image a g a ofo je g g g ROI NOT image ROI NOT ROI Page 104 of 112 Manual for SkyScan CT Analyser v 1 10 2010 BITWISE Image before function BITWISE operation image AND ROI image AND ROI image XOR ROI Page 105 of 112 ROI before BITWISE operation Image after BITWISE operation ROI after BITWISE operation Image inside ROI after BITWISE operation Manual for SkyScan CT Analyser v 1 10 2010 BITWISE function image image SUB ROI image ROI SUB image ROI image SUB ROI ROI ROI SUB image Image before BITWISE operation Page 106 of 112 ROI before BITWISE operation Image after BITWISE operation ROI after BITWISE operation Image inside ROI after BITWISE operation Manual for SkyScan CT Analyser v 1 10 2010 Appendix B Format of the CTAn command line The command line of the CTAn program looks like the following CTAn filename dN s b In square brackets optional parameters are indicated filename full path to the file name or dataset d degree of size reduction of an image in N time s single image opening b start up of the pr
31. Kuwahara There are three things to choose in the configuration dialog for smoothing 2d or 3d smoothing 8d smoothing averages image pixel data vertically in the z axis as well as x and y The smoothing filter tyoe Gaussian Median Uniform Kuwahara The radius of smoothing applied either in 2d or 3d in pixels voxels Morphological operations Morphological operations involve adding or removing pixels voxels to or from the surface of all selected binarised objects called erosion and dilation respectively Open means erosion followed by dilation Close means dilation followed by erosion Meo P olg qical op erations Type Kemet i Fadi The open procedure has the effect of separating objects that are connected at a narrow junction Close is the opposite connecting objects that are in close proximity but initially distinct In the configuration dialog under type choose between erode dilate open and close You can choose to apply the procedure in 2d or 3d You can set the morphological operation kernel to square or round The radius of the kernel is specified in the radius box Page 93 of 112 Manual for SkyScan CT Analyser v 1 10 2010 As with all the plug ins which perform a modifying procedure to the image morphological operations can be applied to either the current image or the ROI In the case of ROI it will treat the ROI as a binarised solid object or objects After apply to please spec
32. S CA Results DATAS CA Results DATAS CA Results DATAS Pai Dael MATAT Dimensions 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 1600 x 1400 LENN s TA New size 800x700 pixels Manual for SkyScan CT Analyser v 1 10 2010 In the open dialog in addition to standard file open dialog functions there are some additional possibilities A selected image can be viewed within the window ina Preview pane Preview is turned on and off by a tick box To find a file of any type from the list of supported image types select the appropriate file type in the list Files of type in the load image dialog box Then only files of that type will be listed and files of other types will be hidden The drop down list Open as allows you to choose between two opening modes Dataset in which the whole dataset will be loaded and Single file in which only the single selected file is opened In the text line starting Image size information about the original size of the highlighted image is shown as well as a final New size if resizing is selected Ticking in the tick box Resize by allows you to reduce image and dataset size by averaging voxel grey levels in a cube of specified size For example resize by factor 2 opens a version of the dataset with 8 times fewer voxels 2x2x2 This allows faster manipulation morphometric measurement a
33. administrator right click option can be used where necessary to launch CTAn for licensing See image below Open Open file location ra Run as administrator You have the option to allow all user profiles in windows the name with which you log on to windows to run CTAn following just one licensing operation To do this go to preferences and the advanced tab at the bottom of the window an option appears with a tick box Page 5 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Allow all users to start the program requires restart and authentication lf the box is ticked it requires closing and restart of CTAn followed by reapplication of the license text data name institute and ID number This licensing must be done by a user with administrator rights Users licensed in this way however do not need to have administrator rights Please note that there is an explanatory document about the licensing of CTAn available for download from the SkyScan web site in the link group for CTAn and CTVol 2 2 Co licensing of the 3D viewing program ANT and CTAn upgrades requiring re authentication After you start this or subsequent versions of CTAn you will find that if you then start any older version of CTAn 1 4 1 0 or previous the program will require registration authentication To run the ANT 3d visualisation program using the same electronic license as CTAn please update it to version 2 4 2 0
34. am is called an instance Position the mouse cursor arrow over the screen object in question and press the left mouse button A tick box activating a function in real time in CTAn Computed tomographic imaging applied to small objects with nominal resolutions pixel sizes in micron or submicron range from 1 100 um Based on multiple x ray transmission images from incremental angular aspects over 180 or 360 This BITWISE operation selects the part of the image that is not in the selected original dataset i e either not in the image or not in the ROI Manual for SkyScan CT Analyser v 1 10 2010 OR This BITWISE operation selects the part of the image that is either in the original image or in the ROI including parts that are in both Pixel Square element of an image characterised by a grey level encoding the image brightness at the pixel location Projection image The projection x ray images are the raw material of the micro CT imaging process These are shadow transmission x ray images where the measured brightness of x rays at each camera detector element is an inverse indicator of x ray opacity in the analysed object along the x ray path from point source to detector element Radio button A small round button in a dialog box next to some text indicating one of several selectable options left click on a radio button and a dot appears in that button and not in any surrounding buttons indicating that a part
35. atus of the plug in shown in real time during batch operation The Dataset list has five columns relating to each selected dataset Dataset the path and filename of the dataset which will be opened and analysed Region of interest the path and filename of the ro region of interest file applied to the corresponding dataset during batch analysis Status the status of the analysis of the dataset shown in real time Results the path and filename of the file where the results of dataset analysis will be written Report the path and filename of the file where the report log will be written listing procedures applied to the dataset Preferences in BatMan Right clicking on the top left corner of BatMan opens a preferences window Move x Close Alt Fa Preferences About TAn The BatMan preferences are a limited set of the preferences in the main part of CTAn One additional preference in under the tab tools Page 80 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Two options are given under the BatMan preferences and Tools concerning the application of preferences previously set in the main CTAn The first option apply global read only CTAn preferences means that on opening BatMan the preferences will be taken from the previous session of the main CTAn The second option apply last used preferences in BatMan will instead on opening BatMan apply preferences a
36. ave Histogram of Size Distribution Savein j mandible_2820 O p eg Date modified Type Name J Size distribution 1 2 22 2010 10 27 AM File Folder E mandible 2820 _ _ dst csw 2 22 2010 10 27 AM Microsoft Office E a File name mandible _ 2820 _dst csv Save as type Tend files csv From Append to file Note that there are tickboxes at the bottom of the window for a appending the text results to a summary file with results of multiple analyses and b the option save color coded image This latter option saves the displayed binarised image with separate binary items displayed with a grey scale linked to their size or other selected Page 60 of 112 Manual for SkyScan CT Analyser v 1 10 2010 display parameter according to the currently displayed histogram This image is saved as a bmp image file in a subfolder given the name size distribution 1 2 as shown in the image above ia Area histogram In the case that either size or length are selected as the parameter for the displayed histogram the area histogram button alternates between total number N and total surface or area S of objects in each category as the y axis unit 123 Show absolute values This button displays the numerical value associated with each histogram bar User defined histogram intervals in the T a histogr ram intervals iT case that length diameter of area equivalent circle is chosen as th
37. closure is defined either in 2d or in 3d Remove broken pores a broken pore is a pore intersecting the boundary of the volume of interest VOI Page 94 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Remove broken objects a broken object is an object intersecting the boundary of the volume of interest VOI Remove inner objects An inner object is defined as an object fully enclosed by space for which the surrounding space is itself fully surrounded by an uninterrupted solid bounding wall Remove outer objects This option removes all binarised objects except those defined as inner objects above Sweep This is the extreme despeckle option First the single the single largest object is identified again either in 2d or 3d Then there are two alternatives a to keep the largest object and remove all other objects or b to delete the largest object and keep the rest Remove all exept the largest object z Remove ject the largest object As with all the plug ins which perform a modifying procedure to the image the despeckle functions can be applied to either the current image or the ROI In the case of ROI it will treat the ROI as a binarised solid object or objects After apply to please specify either image or ROI Page 95 of 112 Manual for SkyScan CT Analyser v 1 10 2010 3D model This plug in will build a 3D model of the current binarised objects inside the curre
38. ction bar In datasets of images created by SkyScan instruments there is a projection image file with a filename ending spr This file is displayed in the top left program window as the Shadow projection bar and simultaneously in the menu there is a new submenu Projection which is also accessible by right button click on the projection image Page 20 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Commands of the menu Projection e Show full area shows the projection image without any modifications e Highlight inactive area highlights in green colour parts of the projection for which there are no crossection images in the dataset e Highlight non selected area highlights in green colour parts of the projection for which there are no crossection images or which are outside the vertical selected range e Show vertical ruler shows or hides a vertical ruler e Show horizontal ruler shows or hides a horizontal ruler Show full area Highlight inactive area Highlight nonselected area Show vertical ruler Show horizontal ruler shadow projection The red line inside the projection image indicates the position of the displayed crossection image in the dataset If you double click the left mouse button at a location on the projection image the crossection image closest to this position in the dataset will be displayed and the red line will move to this position You can measure distance on
39. d avoid out of memory messages However it is still true that many procedures applied to very large datasets will take a very long time So even in a 64 bit system it is recommended to keep to a minimum the size of the ROI datasets that are loaded for analysis into the custom processing BATMAN module and to never load whole datasets into this module Therefore it is strongly recommended that having selected your volume of interest VOI in the scan dataset that in the ROI page in the main body of CTAn you save a new ROI dataset containing only the image data within the ROI see section 7 1 p 30 This should also be resized to the smallest size to enclose the ROI To do this ensure that in preferences and the region of interest page that under save images you select to accumulated ROI bounds and not full image Page 86 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Plug Ins x Name Description Status F Thresholding Segment the foreground from background to binary images I Save bitmaps Save images to new folder iJ 2D analysis Calculate 2D parameters of binary images 2 3D analysis Calculate 3D parameters of binary images J Smoothing Smooth mages and remove a nose The result is a grayscale image f Morphological operations Morrphology based operations i7 Despeckle Remove speckles from images 2 30 model Create 3D surface from binary images i ROI shrink wrap Shrink a AUI to the
40. d distance away Page 47 of 112 Manual for SkyScan CT Analyser v 1 10 2010 from the growth plate and extending several millimeters from this point down the femur shaft So the growth plate is the reference landmark for specifying the VOI including the vertical range Refer to the screen image above illustrating the reference level function applied to analysis of a mouse femur at the distal knee end The projection image top left shows a horizontal red line toward the bottom end which corresponds to the growth plate level as shown also in the crossection image bottom left this is level 231 Note that how a reference level is repeatably selected may depend on a users own interpretation of visual features this is one reason that quantitative analysis of samples from any one given experimental study should if possible be carried out by a single investigator only 4 muis_87_0231 bmp CTAn o gt PORE B uw File name Z position muis_87_0237 bmp 237 line 1 033 mm KE muis_87_0236 bmp 236 line 1 028 mm KE muis_87_0235 bmp 235 line 1 024 mm ya muis_87_0234 bmp 234 line 1 020 mm muis_87_0233 bmp 233 line 1 015 mm raf muis_87_0232 bmp 232 line 1 011 mm KE muis_87_0231 bmp 231 line 1 007 mm sE muis_87_0230 bmp 230 line 1 002 mm KE muis_87_0229 bmp 229 line 0 998 mm muis_87_0228 bmp 228 line 0 994 mm ee muis_87_0227 bmp 227 line 0 989 mm KE muis_87_0226 bmp 226 li
41. d in CTAn The options for colour to grey conversion are e No no conversion Luminance e Luminance this calculates the grey pixel value Red channel from a weighted balance of the RGB values Green channel according to the ratio R G B 0 2126 0 7152 Blue channel 0 0722 e Red channel takes the grey value as the red channel value only e Green channel takes the grey value as the green channel value only e Blue channel takes the grey value as the blue channel value only Raw date file type raw Datasets in non SkyScan formats can be imported into CTAn under the specification of RAW file This is a flexible designation that can be assigned to various non SkyScan formats The specified non SkyScan format can be selected as RAW on opening a dataset as shown in the image below Page 13 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Look in femur10 um scan3_trab_landmark O f em A Name amp femurl0 8um scan3_tr femurl0 8um scan3_tr f ii femurl0 8um scan3_tr amp femur10 8um scan3_tr S femurl0 8um scan3_tr A femurl0 8um scan3_tr femurl0 8um scan3_tr amp femur10 8um scan3_tr amp femurl0 8um scan3 te femurl0 8um scan3_tr E fermiirt f Rium ccan2 tr Date modified 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2 16 2010 6 11 PM 2
42. e Properties Alt Enter Displays the image properties Page 19 of 112 Manual for SkyScan CT Analyser v 1 10 2010 To the right of the list there are two sliders for selection of the vertical range of interest in a dataset Many operations for example animation image analysis etc are applied only to files within the limits of the current selection There is one other way to change the vertical range of the volume of interest VOI double click with the left mouse button on the indicator of selection vertical blue bar between the sliders and the following dialog will appear Selection Direct Analytic 2 pasition near z Select All Top 361 1 573 mm i Apply Bottom 262 1 142 mm OK Here you can manually specify the vertical boundaries of area of interest or restore it to full range by clicking on Select All See 7 2 below for information about the analytic tab and the ROI reference line function For indication that a crossection file is within the volume of interest the colour of the image icon in the dataset bar is varied files within the selected vertical range are shown as yellow or red icons while files outside the vertical range are shown as black and white icons Further the background of the image window is green for active inside the volume of interest and grey for non VOIl images lt is possible to display or to hide the Dataset bar from the menu r View Dataset 4 4 Shadow proje
43. e five stages and corresponding tabbed windows will be referred to as the five pages of CTAn They are The raw image page The Region of interest page The Binary image page The Processed image calculation page Ce 0 MM S The Custom Processing page On opening a dataset several program steps or pages become accessible as indicated by the appearance of buttons under the menu bar E Few mages Regions of interest EA Binay images F Processed images E Custom processing These five pages are also listed under the view menu Page 24 of 112 Manual for SkyScan CT Analyser v 1 10 2010 tz Selection Raw images Alt 1 Regions of interest Alt 2 Binary images Alt 3 Processed imaqes Alt 4 Custom processing Alt 5 with the selection item for specifying the vertical range of the volume of interest appearing at the top above the five pages The five pages of CTAn are ordered in the necessary sequence for analysis and each has specific functionality The VIEW menu items in CTAn View Selection Opens the box for selecting the vertical range of the volume of interest VOI tt View Raw images Initial viewing of images profile and longitudinal resampling View Region of interest Selection and viewing of regions of Alt 2 interest ROI of images saving the ROI dataset View Binary images Selection of the binary thresholds and viewing of resultant binar
44. e graphics card Find the download drivers page and follow instructions to check that the driver on your computer is the most up to date one for your card If it is not update it 2 Goto preferences and the volume tab Click on maximum dimension of texture The word texture refers to the volume rendered model A drop menu will list the pixel dimensions of the model available on your computer see image below In CT Vox the same information is visible under options preferences lt is suggested that you first set it to 256 or the maximum available if it is less than this The memory on board your graphics card limits the available texture resolution Once you are familiar with the operation of volume modeling try the higher available resolutions Note that with 512 or 1024 or above response speed of model viewing might be slow depending on your computer hardware Note that on some older computers graphics cards may not support the software type used for CTAn and CT Vox Open GL 2 in such cases the volume modeling functions will not be available at all Further for technical reasons it is occasionally possible that the maximum listed resolution might not in fact be available This is because some graphics cards such as those aimed at the gaming market divide their onboard memory into two halves Volume modeling in CTAn CTVox cannot divide its memory requirement into halves thus in such a case only hal
45. e histogram option this button opens a dialog box allowing you to Diiis specify the intervals of the histogram of length values This customised set of intervals can be saved Boundary of intervals um ddd Delete All Load GAYE frre di T mam ize distribution Sets the unit on the y axis of the displayed histogram to object size diameter of area equivalent circle a distribution Sots the unit on the y axis of the displayed histogram to object length maximum distance between two object pixels seer meres Lek Scis the unit onthe y axis of the displayed histogram to object perimeter 5 Form distribution Sets the unit on the y axis of the displayed histogram to form factor CY Orientation distribution S ots the unit on the y axis of the displayed histogram to orientation Ee Porosity distribution S ets the unit on the y axis of the displayed histogram to porosity percent area of fully enclosed space in 2d Page 61 of 112 Manual for SkyScan CT Analyser v 1 10 2010 These above functions correspond to the rows of buttons and tabs above the histogram in the analysis window shown below Analysis 2 amp 3 dg 123 S Length LS Form 83 Orientation E Porosity 5 a 0 1 O27 0 3 a Description Abbreviation Value Unit eel Individual 3D object analysis File name obj2b_recl359 bmp 3D analysis Z position Pos Z 1 27462 mrm Save 2D analysis results
46. e that the currently selected dataset level can be set as either the top or the bottom of the vertical VOI range using the right click menu items directly under selection reference Keyboard shortcuts to these two functions are lt CTRL Home gt and lt CTRL End gt respectively Page 49 of 112 Manual for SkyScan CT Analyser v 1 10 2010 9 Page 3 Binary Images Moving on to the third binary images mode half tone binary images are displayed In these images white colour represents areas with brightness within the range of the binary threshold selection solid and the areas outside this selection are black space The region of interest is drawn over the binary image thus the areas inside the ROI remain black and white but the part of the image outside the ROI is highlighted by the current colour of the window background The Histogram bar is opened and there is a new submenu with the same name 9 1 Histogram bar The Histogram bar is divided into two parts At the top is a window with the histogram of brightness distribution displayed Below this is a text table of this distribution a Histogram Sa Ge G g E ai leche Grayscale indexes Hounsfield units Bone mineral density Attenuation coefficient Indes Area rm 2 Total Selected a E 0 D0 6 8198E 002 45 342 E 1 042 0 0610E 001 5 359 2 08 2 97566 0001 1 978 401 28 2 48786E 001 1 654 A 1 6 2 400 E 001 1 6554
47. easurements can be saved to a text file whose filename will default to scan prefix_msr txt Note that the unit of measurement will be taken from the unit correctly selected in preferences general tab under unit e Close Closes the measure tool Page 40 of 112 Manual for SkyScan CT Analyser v 1 10 2010 8 Page 2 Region of interest Moving to the second region of interest ROI step or page allows you to delineate regions of interest on dataset images You can skip this step if you use the default ROI which is set in preferences region of interest as square or round There is a choice of seven ROI types which you can choose from the drop down menu Region of interest Rectangle the rectangle region of interest Square the square region of interest Elliptic the elliptic region of interest Round the circular region of interest Polygonal the polygonal freehand drawn region of interest A aA CO 6H SE Empty the empty region indicates that in the given image there is no set ROI Interpolated the region of interest interpolated from adjacent images Ch In the ROI page each image in the Dataset bar has an icon indicating its type with respect to ROI After loading a dataset all images are initially shown by default as interpolated regions of interest e The default ROI is the rectangular region which has the same size as a dataset image For square images it is possib
48. elative to the origin shown in a tool tip in the selected units of measurement as shown to the right 4 5 Palette bar This bar contains options for changing the appearance and colour of displayed images which while not modifying them at all can be useful for viewing the images Palette x vi J y Images can be inverted by clicking on the Yin Yang icon set to one of four pallets original half tone and two colors and can have their brightness and contrast adjusted Under the pallet drop down menu there is a rainbow like colour bar which displays the colour range of the selected palette Double clicking with the left mouse button on the colour bar restores default values of brightness and contrast You can display or hide the Palette bar from the menu View Palette E Page 23 of 112 Manual for SkyScan CT Analyser v 1 10 2010 5 Five page structure of CT Analyser summary All the world s a stage And all the men and women merely players They have their exits and their entrances And one man in his time plays many parts His acts being seven ages William Shakespeare As you like it In Shakespeare s summary of human life there were seven ages The structure of CT Analyser is not directly analogous to Shakespeare s human life with only five principal stages which appear as separate windows with tabs and which correspond to the normal sequence of steps through the analysis process Here thes
49. ent configuration Further modification of the plug in configuration does not influence the configuration of the same plug in in other tab lists of plug ins About plug in shows a dialog with information about a selected plug in Plug in help shows the help window for a selected plug in BY Page 76 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Batch manager starts a new instance of the C7An program in batch is processing mode and sends to it the current list of operations from the Task list tab each plug in retaining its currently set configuration There is more on the batch manager in the next section Image preview viewing mode in custom processing to view the whole Original image i in the example below Image inside ROI preview viewing mode in custom processing to view only the part of the image inside the current ROI ii in the example below ROI preview viewing mode in custom processing to view only the current 3 ROI itself as a binarised image iii in the example below Note image processing steps such as morphological operations can be carried out on the current ROI in custom processing Subsequent tasks will use the modified ROI i Image ii Image inside ROI iii ROI 11 2 Batch processing mode In the batch processing mode the program starts as a dialog box with an upper and a lower window In the upper window the control elements are displayed simila
50. es of thickness reported only for the VOI Thus if the loaded dataset is large Page 68 of 112 Manual for SkyScan CT Analyser v 1 10 2010 even if the VOI is small then the 3d thickness and separation measurements will take a long time To avoid the analysis taking excessively long use the function at the ROI page to make a new reduced size dataset from the ROI VOI Also from version 1 5 1 9 there is a new type of ROI interpolation between adjacent edited ROI shapes that will be the default The previous method becomes obsolete but when an older prefix roi file is loaded the user will be given a choice of applying the old or the new inte rpolation method File contains the obsolete algorithm of ROI interpolation The new algorithm contains Would you like to apply the new one improved interpol ation of both The final result can be the different non polygonal and polygonal ROIs However when applied to previous roi files the resulting roi will be slightly changed and would for instance no longer correctly enclose an ROI dataset made on the basis of the previous ROI interpolation algorithm In the case of an ROI dataset it would be better to choose the obsolete interpolation method single line text output for automatic creation of table of results from multiple datasets lf single text line is selected results of each analysis are saved as one text line comma delineated The file can be appended to wit
51. ess histogram of the initial 16 bit tiff image is shown Below this histogram slider bars allow you to choose the lower and upper brightness limits between which the images will be transformed into 8 bit grey scale images which you can preview From 16 bits to 8 bits The brightness limits can alternatively be entered by keyboard input into boxes By default these limits are mapped in terms of index of brightness If the file contains calibrated density information you can specify brightness limits in Hounsfield units Page 8 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The button becomes active when you move a slider press it to see the outcome of the brightness selection Press the OK button to proceed to loading of the images with the chosen brightness limits applied Other image formats such as RAW files See section 4 1 below JPG and BMP with bit depths different from 8 bit grey can be internally converted to 8 bit grey level Methods for opening datasets in CTAn In CTAn there are several ways that you can load and open dataset image files drag and drop a dataset image file onto an icon of the CTAn program This operation will open a new instance of the program automatically and all files of the dataset are loaded drag and drop a dataset image file onto any part of the window of an already open instance of CTAn On this action the currently loaded images in CTAn will be unloaded and all the dataset file
52. et at the minimum necessary to fully enclose the ROI at all levels of the selected range This function is also available in the ROI page of CTAn Apply to Image inside ROL Apply to Image inside AOI ha Image inside AOI File format File format BME BMP l JPG Convert to monochrome 1 bit Cony onochirarrie 1 bit Copy shadow projection Copy shadow projection Copy dataset log file Copy dataset log file Insert scale bar Insert scale bar Resize to the RO bounds Resize to the AOI bounds 2d analysis This plug in runs 2d line by line analysis of the ROI part of all dataset images 2D Analysis Add to report Summary results C Individual results C All results Append Summary results to file CAWSACHIVE Narchive_ 11 2steeth tooth datatooth 2d The configuration box allows you to choose whether to output the summary results only the summary list is at the top of the standard 2d analysis report or the table of individual results for each dataset slice or both of these all results Selecting Page 90 of 112 Manual for SkyScan CT Analyser v 1 10 2010 append summary results to file will add the summary results in the form of a line of data for each dataset under appropriate parameter headings this is useful to select if you are analysing multiple datasets for statistical comparison The text output is comma delineated To simplify upload into Microsoft Excel change the extension of
53. etween 2d and 3d is again available in 2d mode the density histogram for each individual image level is output in the text report In 3d mode the integrated density distribution is calculated for all voxels in the volume of interest When 3d is selected the append summary results to file option appears and this allows line by line output of the summary results from one or many analysed datasets in the same way as with the morphometric analysis Four units of density are selectable index grayscale attenuation coefficient Hounsfield units HU and bone mineral density BMD For HU and BMD it is necessary that the appropriate calibration has been done in CTAn otherwise the output unit will revert to index Likewise for attenuation coefficient values to be available this must also have been calibrated either automatically by loading the dataset into CTAn with the dataset log file in place or manually calibrating attenuation coefficient at the binary page 2D space Unit Grayscale Indexes 2D space Grayscale indexes 0D space Grayscale indexes aD DE Hounsteld units Bone mineral density Attenuation coefficient The histogram plug in can be configured to output data in a 2d or 3d space and b in units of grayscale index Hounsfield units Bone mineral density or Attenuation coefficient depending on the availability of the appropriate calibrations Page 101 of 112 Manual for SkyScan CT Analyser v 1 10
54. f 112 Manual for SkyScan CT Analyser v 1 10 2010 RGB to grey The option exists for converting datasets of images with RGB colour information to grey level CTAn can only analyse grey images using alternative conversion methods described above in section 4 1 Text file type Results files from procedures in CTAn including calculations e g 2D 3D measurements are output as comma delineated ASCII text files These can have the selectable extensions of either txt or csv The latter extension is recognised in Microsoft Excel and other spreadsheet programs as meaning comma separated format simplifying the import of these files e g no text import wizard Raw data file type Here the user can specify details of a non SkyScan image format for import into CTAn see section 4 1 Profile line You can set the default position of the profile line function at the raw images page to either a horizontal or vertical line in both cases centrally placed in the image JPEG quality factor Crossection images created when making an ROI dataset or re sliced or MIP images can be saved in either bmp or jpg format The quality factor and degree of image compression is selected in the preferences general tab values less than100 result in some loss of image data Show position inside image Checking this tick box activates the mode in which the mouse cursor when over the projection or crossection images will have its position coordinates r
55. f interest When you call this command the dialog 3D analysis is opened and shows the list of parameters which can be calculated You can select and de select parameters using the corresponding tick boxes Pressing the button begins the analysis and if the flag Auto save result as was ticked a dialog will appear in which you can specify a filename for the text file with the 3d analysis results When text table is ticked the results are saved as a table with each parameter result in a separate line Page 65 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Basic values Additional values Total YO volume Structure model inder Object volume Structure thickness Percent object volume Structure linear density Total VO surface Bg Object surtace Stereclogy Intersection surface Fractal dimension Object surface volume ratio Number of objects Object surkace density Number of closed pores Fragmentation index Porosity Centroid Euler number SIS is Auto save results as text table C single text line Continue Cancel The list of 3D morphometric parameters available for analysis shown after clicking on the 3d analysis button Page 66 of 112 Manual for SkyScan CT Analyser v 1 10 2010 3D Analysis Results a a amp B Dataset fibre sphere_ Number of layers foe Computation time 00 02 21 Description Total YOl volume Object volume Percent object volume Total VOI surtace Object surface Inter
56. f the memory is available Find out by experimentation the resolution level that gives an acceptable image quality combined with control responsiveness Page 26 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Load options Maximum dimension of texture CTE 64 oa O A a 0 Volume of interest 6 2 Launching volume modeling The top button shown below circled in red launches the volume modeling When this green sphere in black wire cube button is pressed a progress bar will indicate loading and where necessary resizing of the dataset and preparation of the volume model Page 27 of 112 Manual for SkyScan CT Analyser v 1 10 2010 With the volume modeling window open the first thing to do is go to the binary page see images below Adjust the binary thresholds with the sliders the binary selection white voxels determines which voxels are included in the volume model Nonselected voxels will be invisible Further selecting different colour palettes can apply colour to the displayed model in all the model modes volume model attenuation MIP The inverse colour Yin Yang symbol button can be pressed to inverse model color snail_rec0276 bmp CTAn File View Image Projection Volume Histogram Help as gt Eene Awn R me OO E me x si diccia Fi ca rec0290 bmp 290 line 12 196 mm
57. ges created by the MIP tool in the x horizontal y vertical and z between crossections planes from the scan of a Microfil infiltrated kidney are shown below Page 35 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Setting a high value for number of projections allows a set of MIP slices to be taken through a selected part or all of the dataset This can be a useful way of displaying quickly the structure of a scanned object in a limited number of MIP slices Kidney micro CT scan 2 Kidney micro CT scan crossection MIP X plane along profile horizontal Kidney micro CT scan 4 Kidney micro CT scan MIP Y plane along profile vertical MIP Z plane horizontal Page 36 of 112 Manual for SkyScan CT Analyser v 1 10 2010 7 3 Protractor tool A protractor tool is available to measure angles on any dataset image Its appearance is shown in the image below To use the protractor hold down the keyboard control key and draw a line with the left mouse button pressed Alongside the line drawn by the mouse movement a second horizontal line will appear and the angular segment between the drawn line hypotenuse and the horizontal line adjacent will be shown To switch control to the other adjacent line keep the left mouse button pressed and release the control key You can switch back to the first line by pressing the control key again The protractor will only be displayed while the left mouse
58. gram ROI view displays the part of the image inside the ROI in black and white and the region outside the ROI under green shading 9 2 BMD calibration by the histogram tab in preferences The histogram tab in preferences allows bone mineral density BMD defined as g cm of calcium hydroxyapatite to be calibrated against the density scales of either Hounsfield units HU or attenuation coefficient Ac ss g om 3 0 06802 The button calibrate allows a choice of calibration of BMD against Hounsfield units or attenuation coefficient Page 53 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Pe a 7 F a i Al Hounstield Units Attenuation Coefficients In the case that Hounsfield units are selected a default button appears which sets a default BMD relationship a published value from clinical CT HU 0 0049 BMD g m3 0 0232 This value can be a default for use of CTAn in clinical CT analysis but will not be appropriate for micro CT due to very different x ray energy and interaction with matter No default value is given for calibration of BMD against attenuation coefficient On pressing the calibrate button a box will open allowing the measured densities of BMD calibration phantoms in either HU or attenuation coefficient to be entered with the corresponding known BMD phantom values The phantom pairs supplied by SkyScan have BMD values of 0
59. h subsequent analysis results The title with descriptions of parameters as column headings is written as the first row at the creation of the new file The second row gives the parameter symbol bone ASBMR or general scientific and the third row gives the parameter unit This results report mode is applicable where multiple samples are to be analysed and compared and the line by line text file is loadable into soreadsheet programs such as Excel When you open this or any other type of CTAn results text file in MS Excel the text Import Wizard appears in the first page you need to set Original data type to Delimited and File origin to Windows ANSI On the second page choose Comma Delimiters and on the third in the dialog Advanced select the decimal separator to point When you finish this wizard you will see a sheet like this e For parameters based on Mean Intercept Length MIL such as Degree of Anisotropy you can select the distance between secants Reducing this distance will make the results more accurate at the cost of increased calculation time In the dialog File Preferences in the tab Advanced you can find the field MIL line spacing Page 69 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Directories Advanced 30 suface construction algonthm MIL line spacing Here in a drop list you can select an option Adaptive where distances between secant lines are measured in microns so for images with different mag
60. he button Temporary files Cvctan TEMP Lay In the opened dialog box specify a path and folder and press the button OK Page 11 of 112 Manual for SkyScan CT Analyser v 1 10 2010 _ m Browse for computer M Select temporary folder from jE Computer 42 o5 C SRecycle Bin gt ARCHIVE i di backup i di Boot ctanTEMP Wb DELL gt d doctemp f ra Documents and Settings gt di mamlTemp d MSOCache y Fa NWRecon From this moment all temporary files created by CTAn will be placed in the indicated directory but this will not affect in any way other programs which also use the same system folder for temporary files 4 1 Conversion of different image formats at opening Two items in the general tab under the preferences relate to the import of different file types They are shown by the red box in the preferences screen copy below Page 12 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Preferences Tools Directores i Advanced General Animation Region of Interest Histogram Volume Image Origin RGB to gray No a Tent file type Raw data file type raw Profile line JPEG quality factor 100 Show position inside image az d RGB to gray this item provides options for converting colour images with RGB red green blue image data to grey format Only grey format images can be analyse
61. he Polygon File Format or the Stanford Triangle Format http en wikipedia org wiki PLY_ file_format e After CTAn installation it is necessary to select the application which will be used for displaying three dimensional models usually it is CTvol exe To do this open the dialog File Preferences and select the tab Tools Page 56 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Preferences BARTEN 6 General Animation Region of Interest Histogram Tools Directories Advanced 3D visualization program a C Skyscan CT vol exe To indicate the application path press the button and in the opened dialog select the visualization program then press the button OK The construction of a 3d model uses one of three algorithms Marching Cubes 33 Double Time Cubes or Adaptive Rendering Marching Cubes is a surface building algorithm based on an explicit hexahedral voxel model developed by Lorensen and Cline 1987 Double Time Cubes is a Marching Cubes type method but with approximately half the number of facet triangles with more smoothed surface detail Bouvier 2000 Adaptive Rendering is a sub voxel smooth rendering method also employed in the SkyScan 3D creator Ant software Note that Marching Cubes is the algorithm used by morphometric 3d analysis in CTAn You can choose the algorithm in the dialog File Preferences on the tab Advanced and the field 3D surface construction
62. icular option is selected Reconstruction Reconstruction is the process by which taking the set of projection images as raw material a dataset stack of crossection images is created using the Feldkamp algorithm and creating the 3D image of the scanned object Resize In this manual resize refers to the procedure at file dataset opening where the image size can be reduced by averaging voxel grey levels in a cube of specified length For example resize by factor 2 opens a version of the dataset with 8 times fewer voxels 2x2x2 This allows faster manipulation morphometric measurement and model building at lower spatial resolution Resize should not be confused with the procedure of creating a new edited ROI region of interest dataset in which only image inside the ROI at each layer is included and all non ROI image is deleted Right click Position the mouse cursor arrow over a screen object and press the right mouse button ROI Region of interest The selected region in a single image indicated by a coloured shape Analysis measurements and model building are performed only on parts of the image within the ROI Page 111 of 112 Manual for SkyScan CT Analyser v 1 10 2010 spin button A field for number entry with up and down buttons to the right which incrementally increase or decrease the number in the field SUB The BITWISE operation subtract SWAP The BITWISE operation swap exchange image and ROI Tab A
63. ify either image or ROI Despeckle The despeckle plug in offers a wide range of image processing options for selecting and rejecting binarised objects on the basis of their size All these variations of despeckle are selectable under type This can be defined again either in 2d or 3d Type Remove black speckles 3D space Volume less than 300 voxels Apply to Image Tea In configuring the despeckle plug in you set the box which is labeled area 2d or volume 3d to eliminate binarised objects either less than or more than a specified number of pixels 2d or voxels 3d This number is entered in the box marked pixels or voxels Again the procedure can be applied to either the image or to the ROI Specify which after apply to Remove white speckles i Here is a brief description of the available variations Hemos act speckles IEMOYVe WALE 10DECRIES Remove pores of despeckle Remove black speckles removes objects that are Remove broken pores black i e thresholded to represent space or Remove broken objects background below or above a specified number of Femove inner objects voxels Remove outer objects TWEED Remove white speckles removes objects that are white i e thresholded to represent solid objects below or above a specified number of voxels Remove pores removes all black space regions that are fully enclosed by white solid voxels En
64. ing page using the button ie a progress bar will appear indicating the loading of the current dataset Important On moving to custom processing the whole current dataset is loaded into memory Even if a volume of interest VOI is selected much smaller than the parent dataset the whole dataset is still loaded It is therefore strongly recommended that you create an ROI dataset at the ROI page a new dataset with reduced size containing only the part of the dataset inside your selected VOI Then open the new ROI dataset and this will both load and run much more quickly in the custom processing environment The custom processing page allows you to apply to the dataset images one or more operations from a list of internal or external modules or plug ins connected to the program Note that this page of CTAn has an open architecture so that a user can contribute his her own analysis routines as external plug ins Internal plug ins are those implementing functions from the core of the CTAn program or You can specify the location of the directory containing external plug ins for CTAn from the dialog File Preferences Open the tab Directories and in the group Plug In Directory press the button Page 73 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Preterences a General Animation Region of Interest Histogram Tools _ Directories Advanced Plug In Directory s CAS kyscan Plugins n In the opened dialog
65. is parameter will be lost e Tolerance this parameter defines the sub pixel accuracy with which the object border is delineated Reducing this number makes the model more smooth and accurate but increases the model file size Con figuration Algorithm Adaptive rendering g Type of file aa m Locality 1 Cancel Tolerance 0 20 Shrink wrap ROI The Shrink wrap plug in provides you with a way to make an ROI boundary exactly following the boundary of a solid binarised object This allows you to then use the object s perimeter as the reference region of interest for example in the study of the internal porosity of an object Page 97 of 112 Manual for SkyScan CT Analyser v 1 10 2010 ROIL shrink wra Mode Shrink wrap JD space Stretch over holes W Diameter 6 voxels s Shrink wrap works in the following way set an ROI around the outside of a study object in the given example a hollow ring of cortical bone Load the dataset into custom processing Set threshold as the first task and select an appropriate threshold value Add then shrink wrap to the task list In the configuration box for shrink wrap after mode choose shrink wrap By clicking the ROI button at the far right above the custom processing window Ss you will see a black binary mask indicating the current ROI Page 98 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Run the task
66. le to set as default a round region of interest entered in quadrate with same sizes as the crossection image Open the dialog File Preferences and the tab Region of Interest set the radio button to Round or Square Preferences are General Animation Region of Interest Histe Default for square images O Square Round A note on terminology region of interest ROI refers to the selected region either Page 41 of 112 Manual for SkyScan CT Analyser v 1 10 2010 fixed shape of free hand drawn on a single crossection image Volume of interest VOI refers to the integration of all the ROIs across all the selected image levels and defines the sub volume of the dataset within which procedures will be performed such as model construction and morphometric calculation The size of the first four fixed shape regions of interest can be changed To do this drag and drop with the left mouse button one of the small squares at the corners of the bounding rectangle of the region of interest The Status bar at the bottom of the program window will display the current size of the bounding rectangle of the ROI Refer to this ROI size if you wish to apply repeatedly VOI volumes of identical size and shape After a release of the mouse button the region of interest size will be set Elliptic ROI Polygonal freehand drawn ROI The whole ROI on a crossection image can also be shifted by drag and drop with the left mouse but
67. les with saving of results to a text file Page 16 of 112 Manual for SkyScan CT Analyser v 1 10 2010 i Handmede Selecting the hand mode allows you to move the image position using left mouse button drag and drop er From the menu item File Preferences you can set the upper value of frequency of image animation ee Frame Rate Visualization 15 frames second Export to AWI 15 frames second This animation speed cannot always be realised With very large sized images memory will become limiting and the speed will become less than indicated Ley Properties In this window information about the image file is displayed pathname filename file size pixel size image width image height and z position in the dataset Note that you can change the pixel size used for morphometric measurements by clicking on change If you then save an ROI dataset this will have the new pixel size lf the path to the file is too long to display completely bring the mouse cursor onto the folder name Under the cursor a tool tip will appear with the full pathname Another way to look through a pathname is to place the cursor in this line and shift the text to the left by using the key Page 17 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Properties File Path C Results OATASE TS mndhs25 Hame mdf 325 0953 jpg Size 1210 KE Date 07 03 2007 21 07 Image Fisel sze 3 24726 um Width 1600 peels 5 1
68. lid objects which can readily occur in this type of adaptive thresholding if parameter values are not correct e g if radius is too small However by running double thresholding first run global threshold with a high value copy this image to ROI reload image and run adaptive threshold then Page 88 of 112 Manual for SkyScan CT Analyser v 1 10 2010 add both images together with the BitWise OR operator the Swiss cheese problem of holes in the adaptive threshold image at thick structures can be obviated You can choose pre smoothing in the threshold configuration box and an associated pixel radius This will apply 2D Gaussian smoothing To apply other types of smoothing you should de select pre smoothing and add the smoothing plug in before the threshold plug in Under the bottom box levels in the threshold plug in dialog you set the lower and upper threshold values If you select default the level boxes will be populated by values found either in the binary page if you are working in the custom processing page with the binary page also open or from any selected roi file if you are in the batch manager BatMan In a batch calculation since usually you need to ensure that the same threshold values are used for all datasets it is better to deselect default and enter the required low and high threshold values The threshold plug in can be run several times if necessary in a task list refer for exa
69. list threshold shrink wrap Then look at the ROI mask again You will see that the original ROI has shrunk precisely onto the perimeter of the cortical bone Note that in custom processing you need to use the S button to see the current ROI you do not get a transparent mask as in the ROI page of the main body of CT analyser The problem of gaps what happens if there is a gap in the cortical bone wall In that case the shrink wrapped ROI will be sucked into the centre of the cortical bone as shown below You can prevent this from happening by selecting the tick box stretch over holes In the configuration box for shrink wrap select stretch over holes and choose an appropriate value for the likely maximum diameter of any hole in pixels Then re run the task list and now where there is a hole the ROI will stretch over the hole and not get sucked inside Page 99 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The other shrink wrap options Shrink Wwrap Fill ut Adaptive In the mode drop menu in the shrink wrap configuration dialog box there are two other functions available apart from shrink wrap These are Fill out select a ROI inside a solid region in the crossection images and the fill out function will expand an ROI from the initial Adaptive with this function if your ROI only partly covers an object the effect will be the same as a shrink wrap of the whole
70. mple to the reload plug in Save bitmaps This plug in saves the current results of the image processing to a new dataset placed in a sub folder with the name of the dataset prefix followed by a number in brackets denoting the number of saved datasets After apply to the configuration box has three image save options Image inside ROI Only the part of the image inside the ROI is saved This function is also present at the ROI page of CTAn If the 5 tick box resize to ROI bounds is ticked the saved dataset will be accordingly resized Image The whole image as displayed is saved ROI The ROI mask is saved in dataset form as a binary image file Under file format bmp or jpg can be selected There are five tick box options Convert to monochrome Images are saved in 1bit format pixels only black or white for smaller file size This option should only be used for binarised images Copy shadow projection A copy of the _spr projection image file will be saved in the created dataset allowing viewing of the projection image in CTAn and Dataviewer software Copy dataset log file A copy of the dataset log file will be saved in the created dataset Page 89 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Insert scale bar A scale bar will be added to the bottom of the saved images automatically adjusted to size Resize to ROI bounds The size XY pixel dimensions of the saved images will be s
71. mum and maximum must be specified e Z size spacing and origin for a single volume RDF the user must specify the Z size number of fields Z spacing and Z origin The Z position of a single field from an RDF will be calculated from the formula Zpos Zorg Zsp n where 0 lt N lt Z size 4 2 Crossection image window When the loading of images is complete the program will show on screen a crossection image below In the menu bar a new submenu Image will appear which contains commands for control of the crossection image display pane These commands can also be accessed by pressing the right mouse button right clicking in the crossection image field Page 15 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Above Lp w Below Down amp Zoom In Zoom Out ha Actual Size p Animation Space Ai Measure m Hand mode Leh Properties Alt Enter Commands of the menu Image om mouse SERES View the image located above n up Below i p MOUSE View the image located below wheel down Shift Zoomin Increase magnification of the image mouse wheel up Shift Zoom Out Decrease magnification of the image mouse wheel down es Fitto Window Fit image size to that of the window ba Actual Size View the crossection image in original size an image pixel is mapped as a screen pixel Measure Opens a tool for manual measurement of straight line distances freehand drawn lines and ang
72. n Length distribution 2o Perimeter distribution I4 Form distribution EF Orientation distribution fo Porosity distribution Page 59 of 112 Manual for SkyScan CT Analyser v 1 10 2010 al Individual 2D object analysis Measures and outputs the 2d morphometric parameters of all discreet binary objects on the current crossection image g Individual 3D object analysis Measures and outputs the 3d morphometric parameters individually for all discreet binary objects in the volume of interest for the current dataset The data report lists parameters for every discreet 3d object 3D analysis Measures and outputs the integrated 3d morphometric parameters for all binarised objects within the volume of interest The data report lists a single summed or integrated value for every parameter for all the binarised contents of the volume of interest eS Measures and outputs the integrated 2d morphometric parameters for all binarised objects on all image slices within the VOI A text file table reports the parameter values for each line lig Save histogram of distribution Saves a text file with the values displayed in the histogram of the currently selected 2d parameter for all discreet binarised objects on the current image level The saved text file takes the filhaame datasetname_dst txt or csv short for distribution When this save distribution operation is selected a window opens as shown below l S
73. n a default temp file is specified automatically and or external plug ins for custom processing see chapter 11 e Advanced Options present here include a surface rendering algorithms for 3d models b line spacing for mean intercept length MIL anisotropy analysis and c various options for 3d morphometric calculation caching datasets useful if loading across a network and an option for licensing CTAn for multiple Windows user profiles See section 2 1 Page 7 of 112 Manual for SkyScan CT Analyser v 1 10 2010 4 Opening files The program can load three types of files BMP JPG TIFF but not all of them are accessible for analysis BMP files all bmp types are loadable for viewing but for analysis only one bit monochrome and eight bit grayscale images will be processed JPG files all jog types are loadable for viewing but for analysis only eight bit grayscale images will be processed TIFF files for viewing and analysis the program supports sixteen bit tiff grayscale images created by SkyScan instruments and software Color images Images in BMP or JPG with RGB color information can be opened for viewing in CTAn but the analysis functions will not be available Conversion to grayscale see section 4 1 below will allow analysis to be performed Images with different bit depth At the loading of 16 bit tifffiles a dialog is opened which transforms the image data to 8 bit for analysis within CTAn A brightn
74. n will begin immediately File saving will be possible after analysis is complete S E When the calculation is complete the following results window will appear Page 64 of 112 Manual for SkyScan CT Analyser v 1 10 2010 individual 3D obiect analvey a amp P Number of objects 212 Object volume mm3 Object surface mm Volume of pores mm 3 Porosity b 0 22075 14 50 783 0 000444 0 200 0 00039 0 00026 0 00024 0 00014 0 00005 0 00005 0 00002 0 00002 0 04725 0 03506 0 03660 0 02609 0 02123 0 01478 0 00903 0 01152 0 00000 0 00000 0 00000 0 00000 0 00000 0 00000 0 00000 0 00000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 00002 0 00854 0 00000 0 000 0 00001 0 00551 0 00000 0 000 0 00000 0 00230 0 00000 0 000 0 00000 0 00218 0 00000 0 000 1 2 a 4 a 6 Fi a g 10 11 15 4 Note that by clicking on any of the parameter headers such as object volume changes the order of the displayed objects so that objects are then displayed in either ascending or by clicking again descending order of the selected parameter The three buttons at the top of this results window for individual 3d parameters allow saving and printing of the analysis results and closing of the results window 10 5 Analysis of all objects in 3d Analysis 3D analysis initiates three dimensional 3d image analysis of R binary selected objects white colour within the volume o
75. nalysis of a typical busy laboratory Page 3 of 112 Manual for SkyScan CT Analyser v 1 10 2010 2 First start up of the program The program does not require special installation on the computer it runs from the single CTAn exe file which can be copied into any directory on the hard disk or it can start from a network drive The first start up should be under a user profile with administrator rights Subsequent start ups have no such restrictions and can be carried out from profiles with limited rights Depending on what type of CTAn license is installed by the user at the given moment the program can work in one of the following modes e demonstration mode established by default in which some functionalities are disconnected e limited 30 day s full functionality of the current version of the program e unlimited To obtain a limited or full license it is necessary to register the program at SkyScan to do this email to info skyscan be the following personal data e the name of the user e the title of the organization e the product ID number of the program you see this at the first start up of the downloaded CTAn On the basis of these data the license file CTAn lic will be generated and you will receive this file by e mail from SkyScan This file needs to be copied into the directory from which the CTAn program will be started up With your license file in place at the next start up of C7An a dialog bo
76. nd separation are selected additional options appear at the bottom of the 3d analysis dialog for saving colour coded images of structure or bone thickness and separation The resultant images are saved in a new directory in the same format as new datasets created by the save bitmaps plug in To view the colour coded thickness open the dataset in SkyScan Dataviewer Under the colour drop menu choose color 1 or 2 Then the bar under Color data range will become coloured At first the image will usually look very dark with little visible You need to move the upper color slider and move it down from its default value of 100 In the example below it is reduced to 14 Adjust the color slider to obtain a good range of colors corresponding to thickness BY DataViewer evelyn_tooth_rec0324 bmp Actions View Options or p i Color Data range dd Inverse Color 1 Smooth Position Hwiew in 2D mode 461 432 324 0 0 Zoom 100 Angle 0 Smoothing The smoothing plug in is normally applied to grey level non binarised images although you can apply it to binary images also If you do the resultant images will no longer be binary but will have several grey levels Simply repeating the threshold plug in easily returns the images to binary This way you can smooth binary images if required Page 92 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Gaussian Radius Median A adius 4 Uniform
77. nd model building at lower spatial resolution The factor of diminution is from 2 to 16 by length 8 to 4096 by volume The locating of each image file takes time and therefore when the dataset size is large or the dataset is loaded from a remote drive across a network the time taken to load image files can become significant If you have enough free space on the local hard disk you can reduce this time by activating a caching option after which the files will be read only once into a temporary file and then CTAn will work only with this temporary file not wasting time accessing the original files To do this call the dialog File Preferences go to the tab Advanced and tick the Cache images box Page 10 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Perform the advanced three dimensional stereology E Restrict the thickness calculations to within the VOI only This caching begins to work with the next opening of a dataset so ifa dataset is already open when you select caching reload it The caching option is applicable only for the following files BMP 1 and 8 bits TIFF 8 and 16 bits JPG 8 bits e During operation the program creates temporary files in a specified directory You can specify where on the hard disc to create temporal files avoiding locations with insufficient space To do this select File Preferences go to the tab Directories and under the heading Temporary files press t
78. ne 0 985 mm 5 KE muis_87_0225 bmp 225 line 0 980 mm B KE muis_87_0224 bmp 224 line 0 976 mm T 5 L muis_87_0223 bmp 223 line 0 972 mm w 2 m E muis_87_0222 bmp 222 line 0 967 mm E 2 E muis_87_0221 bmp 221 line 0 963 mm F w rane OF 1990 bee IIN Kaw N GEO marat A Palette x lo iginal Selection Z pasition Reference 231 1 007 mm Offset 0 218 mm 4 Height 300 1 307 mm Cancel qQ 30 301 601 Inbox Microsoft f Micro CT papers A muis_87_0231 b Above the growth plate level in the projection image the clear region not highlighted in green marks the selected vertical VOI Double clicking on the vertical blue VOI selection bar top far right opens the dialog box titled selection visible below left in the above figure In this box the analytic tab shows three fields for number entry with up and down buttons spin buttons entitled reference offset and height The reference level here is the growth plate level 231 To the left of the spin box the height of this level in the dataset is shown also 1 007 mm Next is the offset the Page 48 of 112 Manual for SkyScan CT Analyser v 1 10 2010 distance in lines here 50 or 0 218 mm from the reference level to the bottom limit of the vertical VOI Note that this value can be positive or negative with a nega
79. nifications this distance expressed in pixels will be different By choosing Fixed the distance between lines is expressed in image pixels and calculation time will be independent of image pixel size When the analysis is finished the dialog 3D Analysis Results will appear in which the results are displayed as a table with a blue background and have units of measurement as specified in File Preferences General Unit lf before the beginning of the three dimensional analysis the Auto save result as box was ticked then at the bottom of the results table the filename of the results text file will be displayed such as prefix__3d txt In this case the icon is displayed to the left of the text filename When you left click this icon the 3d results text file will be opened and displayed with Windows Notepad PL 4P The auto saving of results i done in fibre sphere 1 sd tet You can save the results of 3d analysis as a table text file by pressing the E button Save results or as a single comma delineated text line by pressing the button Append results to file If you click the left mouse button on the Print results icon the analysis results will be printed Pressing the button Close window will close the dialog window qe Page 70 of 112 Manual for SkyScan CT Analyser v 1 10 2010 10 5 2 Advanced options for 3D morphometric calculations In the advanced tab of the preferences there are four tick box i
80. nt VOI volume of interest Configuration Algorithm Double Time Cubes Type of file ctm Cancel Three things need to be specified in the 3D model configuration dialog box After algorithm please choose between the following options Double time cubes a smoother version of Marching Cubes Refer to Bouvier 2000 Marching Cubes 33 A recent improvement on the original Marching Cubes algorithm an explicit model showing detail down to individual voxels good for finely detailed objects Adaptive rendering An algorithm developed by SkyScan in which a smooth faceted surface is fitted by sub voxel contouring This model type gives the most smooth realistic surfaces but it is not as ideal as the Marching cubes Double time cubes methods for very fine detail After type of file you can choose between the following file formats for the created 3D model file STL Stereo lithography model format a standard type accepted by much commercial software such as finite element analysis software e g ABAQUS ANSYS Materialize P3G A SkyScan model format Where model size is small to medium this format is useful the file size is relatively small and an additional smoothing option is available in CT volume for p3g models CTM A SkyScan model format Model building in the ctm format is faster than in p3g which can be useful for large models such as from high resolution scans However ctm models do no
81. object Reload Image Region of Interest The reload plug in reloads the open dataset into custom processing within the run of a task list without deleting the currently selected ROI in the task list Note that the ROI set during a task list is temporary and cannot be saved after the task list is complete An example of the use of reload is in the analysis of a metal implant in bone First set a high threshold to binarise the metal only Then run shrink wrap set to image convert The binary image of the metal implant now becomes the ROI Then run reload Now set a threshold suitable for bone The ROI can be dilated by say Page 100 of 112 Manual for SkyScan CT Analyser v 1 10 2010 5 pixels to set a boundary of the ROI which is exactly 5 pixels distant from the metal implant surface Now if you run 3d analysis the intersection surface will tell you how much crossectional area of bone is intersecting the ROI surface at an exactly specified distance e g 5 pixels from the metal surface This approach using varying pixel distances from the metal surface could be used to assess the status of bone around a metal implant and how well the implant was secured in the bone As with several other plug ins the reload function can be applied to either the current image or the ROI Histogram The density distribution of the loaded dataset can be output by the histogram custom processing plug in Selection b
82. ogram in batch processing mode all remaining parameters are ignored Examples of use C Skyscan CTAn exe C Results img0100 bmp the file img0100 bmp is opened and in the case that it is part of a dataset all files of the dataset are loaded C Skyscan CTAn exe C Results img bmp the files of a dataset with the prefix of the name img are opened C Skyscan CTAn exe C Results img0100 bmp s only the file img0100 bmp is opened C Skyscan CTAn exe C Results img omp s d2 the first file of a dataset having the prefix img is opened with factor 2 size reduction C Skyscan CTAn exe b The program is started in batch processing mode Page 107 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Appendix C Glossary of terms used in the CT analyser manual AND This BITWISE function causes the resultant image to correspond to only the parts or pixels of the image that are the same in both the image dataset and the ROI An example of this is the useful function image image AND ROI which has the effect of removing all parts of the image outside the ROI providing the ROI is a binary mask ASBMR American Society of Bone and Mineral Research This organisation published a naming system or nomenclature for bone histomorphometric parameters Parfitt et al 1987 in which a consistent system of abbreviations were given to parameter names and their components Examples are Tb Th for trabecular thickness BS BV for bone s
83. om text Custom logo Page 83 of 112 Manual for SkyScan CT Analyser v 1 10 2010 2D analysis results a text table of the results of two dimensional analysis of the current single image only Summary results of 2D analysis a text table of the results of the line by line measurement of 2D parameters summarised for every image level 3D analysis results a text table of the results of three dimensional analysis most recently produced on the volume of interest from the dataset Crossection image the active image shown in the raw images window Shadow projection the image of the projection shown in the shadow projection bar Custom text you can open a box to enter your own text and format the text by selecting font type size etc Custom logo your own company or university logo can be added to the report just copy it as a bmp image named ogo bmp in the same directory as CTAn Left button click inside the field of a printout item makes it active and draws a dashed rectangle around it and shows that item title in the Layout Item list The layout item can be moved by left mouse button drag and drop To change the size of a printout item you need to make the item active left mouse click on it At the corners of the dashed rectangle surrounding the active item you can find small black squares Drag and drop one of these squares with the left mouse button to change the size of the rectangle After
84. or SkyScan CT Analyser v 1 10 2010 slower than for ctm models iii the model file type stl widely used by 3d imaging and stereolithography software is saved with spatial information encoded in the unit mm um inch pixel chosen in File Preferences at the General tab in the field Unit You can tick in the box at the bottom of the create 3d model dialog to automatically launch the associated program e g CT volume to show the model immediately after the model building is complete Note The type of 3D model surface rendering is chosen in File Preferences at the Advanced tab see below Models created by each rendering algorithm can be saved in any of the three model file types Hat Create 3D Model Save in mandible_2820 O g e g Name Date modified Type di mandible 2620 bone_binary 1 22 2009 4 03 PM File Folder di mandible 2620 enamel_binary 1 8 2009 11 02 AM File Folder di mandible_2820__sagittal 17 8 2009 11 02 AM File Folder p File name mandible 28270 p3q Save as type 4g CTM files ctm PLY files ply The three 3d model file types are STL P3G CTM and PLY STL Stereolithography an industry standard surface rendered model useful for inputting into other software P3G A flexible format allowing smoothing of the surface in the CT volume viewing software CTM A general purpose model format with good stability at very large model sizes PLY A computer file format known as t
85. oving to the morphometry page a menu and bar with the title Analysis will appear to the right of the crossection image window in which you have access to morphometric analysis commands 10 1 Analysis bar The Analysis bar is divided into two parts At the top is the histogram of the distribution of a 2d image quantitative parameter note the geometrical x axis scale The parameter is indicated on the tab above the histogram there are six to choose between object size perimeter etc The data shown here and in the table just below the histogram relate only to the currently open single crossection image Each histogram bar relates to a parameter value range and has its own colour In the image window objects are correspondingly coloured according to their value of the currently selected 2d parameter You can customise the colour pallet using the slider bars At the bottom of the analysis bar is a table with the 2D analysis results of the selected image You can use the buttons and tabs of the Analysis bar to access commands located in the Analysis menu You can also open this menu by right mouse click anywhere in the analysis window Individual 2D object analysis Indrvidual 3D object analysis 3D analysts Save 2D analysis results 10 2 Commands of the Analysis menu pal fe cave histogram of distribution we Area histogram listed by right click in the analysis histogram pane mw Size distributio
86. ption is provided here of the internal plug ins in the custom processing and batch manager modules of SkyScan CT analyser To start with a very important recommendation Unlike in the main body of CTAn datasets are loaded to memory RAM as two copies in custom processing A very large dataset for instance a 4k scan reconstruction cannot be loaded into custom processing It may however load into the CTAn main body All procedures you carry out in custom processing will work most quickly and efficiently with datasets of the smallest attainable size Therefore you should make ROI datasets and load these into custom processing do not load full datasets into custom processing In a 32 bit operating system datasets over a certain size loaded into custom processing will cause an out of memory error when any 3d image processing operation is run In a 64 bit system the upper limit of available memory is not restricted to 2 3 GB as in 32 bit systems but is limited by the amount of RAM present in the computer However the RAM available to CTAn is significantly less than the total in the computer due to the distribution of resources that goes on in a Windows computer which limits the RAM available to a single process such as CTAn So ina 64 bit system it is advisable to have at least 8 GB of RAM in the computer in order for CTAn to have a good working amount of RAM With a 64bit system and a suitably large amount of RAM you shoul
87. ptive median C High Adaptive mean C Adaptive mean of minimum and maximum values Cancel Page 87 of 112 Manual for SkyScan CT Analyser v 1 10 2010 between three options as shown below Having chosen a variant of adaptive thresholding you configure the adaptive thresholding by a choosing to run the adaptive thresholding in 2d or 3d space b setting the correct background colour c choosing a pixel radius of image processing and d choosing a constant offset value Threshold Type Adaptive mean of min and mas values 2D pace Background Radius A Dark Constant O Pre processing Pre srnoothing Radius z Pre threshaldinig Levels Default levels ere Ef High 254 Cancel The radius defines the circle within which the threshold is calculated using one of the three methods median mean mean of min and max The constant applies an offset to the minimum density contrast recognised by the thresholding Increasing constant can remove noise associated structures Note that a pre threshold can be applied The pre threshold effectively delineated a region of interest within which adaptive thresholding is applied All pixels outside the prethreshold white mask are excluded from the adaptive thresholding and set as black space A certain amount of trial and error is needed to get a correct result Be careful to avoid the appearance of false voids inside so
88. re CTAn exe is located If this Jogo bmp file is absent a default SkyScan logo is provided The drop menu Alignment in the group Snap BAAI 2 X specifies which of the corners of a rectangular layout item will be taken as the anchor binding it to the square grid The pitch size of this grid is indicated in the Size field You can type here any text In the Layout Item group you can select an active printout item from a drop list When the box Hide is checked the active layout item is not displayed and is also excluded from the printed report what you see is what you get Likewise the border around an active item will be drawn if the Border check box is ticked otherwise not Pressing the button in the Print lls 4 Layout dialog you can specify page size and C Hid C Border Edt orientation select the active printer and Hg change its properties Layout Item gt lal fal Print Setup Printer Name HP Lasevlet 1100 MS v Status Ready Type HP LaserJet 1100 MS Where LPT1 Comment Paper Orientation Size Ad Portrait Source Automatically Select Landscape Layout Item The Layout Item drop list can contain the Histogram of distribution following items 2D analysis results Summary results of 2D analysis Histogram of distribution the image of the oe sem histogram of distribution shown in the Analysis Shadow Projection bar 2d parameters from current image Cust
89. releasing the mouse button the printout item will be drawn with its new size marked as a dashed rectangle The check box Page border shows or hides a border around the printout page The button sends your printout page to the active printer The button Reset All resets the position of all printout items This command allows you to return items to within the limits of the visible area of the page if for any reason any printout items are out of the page boundaries The button closes the Print Layout dialog and saves all modifications whereas the button closes the dialog without saving any changes Page 84 of 112 Manual for SkyScan CT Analyser v 1 10 2010 References Feldkamp LA Davis LC Kress JW 1984 Practical cone beam algorithm J Opt Soc Am 1 6 612 619 Parfitt AM Drezner MK Glorieux FH Kanis JA Malluche H Meunier PJ Ott SM Recker RR 1987 Bone Morphometry standardization of nomenclature symbols and units J Bone Miner Res 2 6 595 610 Dennis J Bouvier Double Time Cubes a fast surface construction algorithm for volume visualisation Unpublished report University of Arkansas 313 Engineering Hall Fayetteville AR 72701 USA 2000 Lorensen WE Cline HE 1987 Marching cubes a high resolution 3d surface construction algorithm Computer graphics 21 4 163 169 Page 85 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Appendix A Description of plug ins in custom processing A descri
90. rly to the elements in the Plug Ins bar in the custom processing page Above the upper window are three tabs Task list shows the list of operations selected from internal and external plug ins which will be applied to the dataset in the sequence shown top down Internal shows the list of internal plug ins Page 77 of 112 Manual for SkyScan CT Analyser v 1 10 2010 External shows the list of external plug ins loaded from the directory specified by File Preferences Directories Plug In Directory To control the task list use the buttons located to the right of the upper dialog window adds the selected plug in from the Internal or External tab to the list of plug ins in the Task list tab deletes a highlighted plug in from the list on the Task list tab shifts the selected plug in up by one line on the list changing the sequence of execution of plug ins on the Task list tab shifts the selected plug in down by one line on the list changing the sequence of execution of plug ins on the Task list tab reads from the disk a list of plug ins ctt file and shows them on the Task list tab saves to disk the list of plug ins shown on the Task list tab plus the configuration of each plug in as a cit file Task list 4 intemal aie External Hame Description Status Thresholding Segment the foreground from background to binary images Remove I Despeckle Remove speckles from image
91. rmat of the CTAn command line 107 Appendix C Glossary of terms used in the CT analyser manual 108 End of manual 112 Page 2 of 112 Manual for SkyScan CT Analyser v 1 10 2010 1 Introduction CT analyser CTAn is an application for deriving quantitative parameters and constructing visual models from scanned datasets obtained with SkyScan micro CT instruments CTAn allows real time volume rendered model viewing surface rendered models are also created by CTAn for viewing in another program CT Volume CTVol Quantitative measurement is made both of densitometry voxel attenuation coefficient or calibrated density and of morphometry the latter based on a segmented black and white image Thresholding or segmentation is done by simple global or by adaptive methods Tools are provided for highly flexible volume of interest VOI delineation including positioning relative to structural landmarks the essential starting point of all 3D quantitative analysis Modified datasets either restricted to the VOI or following image processing can be written as new datasets from CTAn A set of image processing tools including Boolean operators is also provided CT Analyser represents a comprehensive environment for obtaining 3d model images and quantitative data from micro CT scan datasets Reporting of data is flexible including spreadsheet e g Excel ready data table output and suited to the requirements of high throughput a
92. rther four buttons representing various functions These will be described in this chapter on the raw images page In this mode the following commands become accessible File Export to AVI file this command allows you to create from the dataset images within the volume of interest an animated AVI file by using one of the video codecs installed in your system After you select a file name for the animated file this system dialog will appear Video Compression Contes Full Frames Uncompressed v From the Compressor list select one of the video codecs which gives you the required degree of compression and image quality Note It is not guaranteed that all compressors from the list are available on your computer Recommended video compression codecs are Microsoft Video 1 and Cinepak Codec by Radius both should be set to 70 100 quality lower value for smaller avi file size e To set the frame rate of the output animated AVI file open the dialog File Preferences Animation and go to the field Export to AVI Page 31 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Frame Rate m I Visualization frames second Export to AVI frames second 7 1 Profile bar The profile bar turns on a number of functions such as density line profile longitudinal image cuts through the dataset and maximum intensity projection MIP image generation from different angles To activa
93. ry file and then CTAn will work only with this temporary file not wasting time accessing the original files Contrast Contrast is an important parameter of image quality and relates to the range of brightness levels in the image of an object both crossection and projection images A large range between dark and light regions of an image corresponds to good contrast Note however that dark and light regions should not saturate Good contrast in projection images is needed for it to be possible to reconstruct well contrasted crossection images Contrast in projection scan images is optimised by adjusting the x ray source applied voltage and filter for example reducing voltage to increase sample absorption if contrast in projection images Is too low COPY A BITWISE operation that copies one dataset onto another for instance ROI COPY image will make the ROI become an exact copy of the currently loaded image Note this operation replaces the previous function image copy that in earlier CTAn versions was listed under the shrink wrap function Crossection image The dataset produced by Feldkamp cone beam reconstruction of the x ray projection images consists of a stack of crossectional images consisting of pixels or voxels with brightness expressed as grey level These images can be considered as slices with a thickness of the voxel size in the case of every slice reconstruction or multiples of the voxel size if
94. s J J Despeckle Remove speckles from images ROI shrink wrap Shrink a AOL to the boundary of a binarised object F Morphological operations Morphology based operations I Despeckle Remove speckles from images Import I Sronnthina Smooth imanes and rere a nnise The reslis a noranecale imane 4 i Export Configuration About Dataset Region of interest EH C Results AYC_fibula AVC Ameterdam_fibulas 2011_scane fibl Lakfib_Tla_vois C Results AYC_fibulaXAYC Armest i GE C R esulta AYE Abula AW C Amsterdam_Abulass20l1_scansshbi A ashb_ ra_wol C Results AVC_fibulaSAyC amet ra C ResultsSAYOC_fibulaSAYC Amsterdam_fibulass2011_ecanssibeLafib_2la_vork C Results AYO_fibulaSAC Amet ea C Results AYOC_fibulaSAYC Amsterdam_fibulas 2011_scanesibeAasfib_2ra_ vai C Results AYO_fibulaSAyC Amet ra C Riesults AYOC_fibulaSAC Amsterdam_fibulas 2011_scansshib4la fib_dla_vork C Results AYO_fibulaSAyC Amet Ew C Results AYC_fibulaSAYC Amsterdam_fibulas 2011_scanssib4Aasfib_4ra_ voi Ee C Results AYC_fibulaSAC Amsterdam_fibulass2011_scansshibblasfib_5Sla_vork a C Results AYC_fibulaSAYC Amsterdam_fibulas 2011_ scansfibbRasfib_5ra_ voi EE C Results AYC_fibulaSAYC Amsterdam fibulas42011_ scansshibblasfib_Bla_vor E C Results AYC_fibulaSAYC Amsterdam fibulas42011_scanssfibbRasfib_Gra_ voi Move Up Move Down Results C Results AYO_fibulaSAy Amst C Results AYC_fibulaSAy Amst C Results AYO_fibulaSAyC
95. s of the dragged and dropped image will be opened CTAn can have only one dataset open at any one time specifying the full path and file name of a dataset in the command line Appendix A This mode can be used for program calls or in batch BAT files On this operation a new instance of CTAn automatically opens the specified dataset opening dataset images from the CTAn open menu For opening dataset files from the CTAn menu select the command Ctrl H O File Open z Look in Ji mdf325 Name ee mdf_325_0775 jpg mdf_325_0776 jpg ee mdf_325_0777 jpg mdf_325_0778 jpg mdf_325_0779 jpg mdf_325_0780 jpg mdf_325_0781 jpg mdf_325_0782 jpg mdf_325_0783 jpg mdf_325_0784 jpg mdf_325_0785 jpg M dF DIE ATOE tee File name Files of type Open as Page 9 of 112 Date modified 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM 6 2 2006 5 35 PM era one 30 RA mdt_325 0 80 jpg All supported files bmp jpa tif Dataset ki Image size 98 emn Size 1 285 KB 1 286 KB 1 286 KB 1 285 KB 1 285 KB 1 286 KB 1 288 KB 1 290 KB 1 292 KB 1 293 KB 1 295 KB 1707 FD 16001400 pixels Folder path C Results DATAS G Results DATAS G Results DATAS C Results DATAS C Results DATAS CA Results DATAS C Results DATAS CA Results DATA
96. s set in the previous BatMan session Page 81 of 112 Manual for SkyScan CT Analyser v 1 10 2010 12 The printed report In the dialog opened by the command File Print Layout you can customize a printed analysis report see below In the top part of this dialog box the report page is displayed in a reduced form In the lower part are the functions which select and configure items for the report page Print Layout Realy hq Study Rey Crug Discovery Gun Study Director Or J Smith Jan 9 2099 Hi f il Vil Mil Ml Ii I p I i gi oe Fj I I L j Margins mm Left 6 E Alignment left top vi Right 6 Bottom 5 Size rm 1 Layout Item _ Page border OK 2D analysis results Hide Border In a group Margins on the dialog Print Layout you can specify the size of indents from edges of the page expressed in millimeters In the list of layout items there are Custom text and Custom logo When you select Custom text from the Layout Item list the button will appear Pressing this Page 82 of 112 Manual for SkyScan CT Analyser v 1 10 2010 button will open the Custom text dialog where you can enter any text which will be displayed on the printout page The item Custom logo shows a logo which is stored as the file logo bmp This file must be located in the directory from which the start up of the program is initiated i e whe
97. section surface Object surface volume ratio Object surface density Fragmentation index Centroid x Centroid y LCentroid 2 Structure model inde Structure thickness Chriockioire lieaor daarnet Abbreviation TV Obj Ob we Ty TS Obj 5 L5 Obj SO by Ob S T Fr Crd Crd Cid Value 0 54990 0 22192 40 35698 3 60252 1454102 1 54600 bo 52a 26 44209 4 06507 0 03000 0 00406 1 23391 2 33050 0 09574 A WLRAR 4 The auto saving of results is done in fibre sphere Sd bt button The window displaying results after running the 3d analysis function The in the bottom left of the window opens the text file containing the full results listing A part of this text file is shown in the image below Page 67 of 112 Manual for SkyScan CT Analyser v 1 10 2010 phere_3d txt Notepad File Edit Format View Help CT Analyser Version 1 8 1 2 Date and time 11 06 27008 13 26 Operator identity phils Computer name PHILS PC Computation time 00 02 21 Dataset fibre_sphere_ Location C ARCHIVE Archive_nonbi omed fibres obj2b__rec 1 fibre_sphere Description Abbreviation Value Unit Number of layers 287 Lower vertical position 0O 73850 mm Upper vertical position 1 75394 mm Pixel size 3 55048 um Lower grey threshold 128 Upper grey threshold 255 Total VOI volume Tv 0 54990 mm3 Object volume Obj V 0 22192 mmA3 Percent object volume Obj V Tv
98. t have the option for smoothing in CT volume which is available for 03g models PLY A non SkyScan format used in other 3D visualisation software Please note that the model algorithm Marching Cubes Adaptive rendering etc and model format P3G CTM etc are not the same thing this means that models made by any of the three algorithms can be saved in any of the three available formats Page 96 of 112 Manual for SkyScan CT Analyser v 1 10 2010 However models made by adaptive rendering should be saved in p3g format in order to visualise a smooth surface Note also that the unit drop menu box is only applicable to the STL model format which is the only format which encodes absolute spatial distance information For STL files choose between voxel um mm and inch The P3G and CTM formats always use voxel Selecting different distance units for STL models can have an effect on visual the size of the model on opening in CT volume If necessary adjust the cube size in stage properties in CT volume to obtain an appropriate viewing size for the model In the case of selecting the adaptive rendering 3d model algorithm two further parameters need to set e Locality this parameter defines the distance in pixels to the neighboring point used for finding the object border Increasing this value allows jumping through noise on the object border but small objects often created by binarisation of noise with size less than th
99. t structures If the colour is set to the colour of the maximum density then the process will generate instead the minimum intensity projection revealing low density inclusions e Depth of projection This sets the number of image slices in the chosen plane that will be sampled centered around the current crossection in the case of horizontal view and the red line in the case of along profile being selected With along profile selected the depth of projection is displayed in real time as a shaded region centered along the red line e Number of projections The selected projection depth can either be sampled as a single MIP if number of projections is set to 1 the default value or can be divided into a selected number of multiple slices When the horizontal z axis MIP is selected the image will sample all the crossection levels of the open dataset When along profile is selected a box with the title depth will appear in which you should enter the number of pixel slices to be sampled orthogonally to the profile line The region thus selected for MIP imaging will be shown interactively as in the white central band in the image below the same as in the tool for angular reslicing see above Note again that the profile line can be either a default centrally placed horizontal or vertical line as set in preferences general tab or a line drawn freehand in any direction and of any length Examples of the ima
100. t the top of some windows and dialog boxes are tabs resembling the tabs on the top of folders ina paper filing cabinet allowing easy access to multiple pages of information by left clicking on the tabs Tool tip A tool tip is a small text window that opens under the arrow cursor controlled by the mouse For example tool tips give explanations of menu buttons and icons and also give x y position coordinates when the cursor is positioned over either the crossection or the projection images subject to preference setting VOI Volume of interest The integration of all ROIs within the vertical selected bounds of the dataset Voxel A 3D pixel an image element with finite x y and z dimension Usually datasets are composed of isotropic voxels that is voxels whose x y and z dimensions are identical When discussing micro CT images it is probably better to talk of voxels than pixels XOR The BITWISE operation XOR selects the part of the image that is either in the original image or in the ROI but excluding any part that was in both the original image and the ROI Page 112 of 112
101. te The result is a grayscale image 42 Morphological operations Morphological operations iJ Despeckle Remove speckles from images 2 30 model Create 30 surface from binary images 2 ROI shrink wrap Shrink a AOL to the boundary of a binansed object Reload Reload images or AOI 4 Histogram Image histogram External shows the list of external plug ins loaded from the directory specified by File Preferences Directories Plug In Directory Output Report here you can find the paths and filenames of the text files with the analysis results Output file and the report or log of operations done Report file Both files are created in the dataset folder each time a task list is run on that dataset and they have the same prefix as the dataset images followed by the double extension C TAn txt or C TAn og Both output text files have the same set of options The button opens this file for viewing Plug Ins x Task list 2 Internal External ig Output Report Output file CAR esults peg rat2_2 ctan tet Append Show Report file CAR esults jpeg rat2_2 ctan log Append Show The live flag Append indicates that the information will be added to the end of the results output or the log report file file Otherwise this file will be overwritten after the execution of a single plug in or a list of plug ins When the switch Show is on the corresponding text file will be automatically opened for
102. te the profile bar click on the profile line button at the top button bar circled in red File View Image Projection Help When this bar becomes active a red line appears on the crossection image This line can be re drawn anywhere on the crossection image by left mouse drag and drop with its beginning marked by a small circle In a bar to the right of the crossection image a grey level profile along this line is drawn and the left hand end of this profile corresponds to the beginning of the line with the small circle trod al Page 32 of 112 Manual for SkyScan CT Analyser v 1 10 2010 On the panel above the profile graph two scissors icon buttons are located which give access to the following commands Save profile saves a text file with the results of the density profile line these include the start and end pixel coordinates the line length in pixels and the grey level listed at every pixel along the line Cut model creation of a single longitudinal section cut along the profile line Fi through the dataset within the limits of the region of interest In the opened dialog box the cut is displayed and you can save it by pressing Ba on the button Save image Reslice model creation of a new set of images consisting of longitudinal Fe section cuts along lines parallel to the profile line The parameters for constructing such a longitudinal section dataset are set in the dialog box which appears
103. tems at the bottom these are e Perform the advanced 3 dimensional stereology Selecting this option adds a list of parameters related to the mean intercept length MIL calculation of anisotropy and the MIL tensor to the end of the 3d analysis report e Restrict the thickness calculations to within the VOI only Selecting this option reduces the time taken for 3d thickness and separation calculation by the distance transform based local thickness method e Cache images requires the dataset reload this option is discussed in section 4 under opening of datasets e Allow all users to use the program requires restart and authentication this option is discussed in section 2 under licensing and starting of the CTAn program E Perform the advanced three dimensional stereology E Restrict the thickness calculations to within the VOI only Allow all users to start the program requires restart and authentication Page 71 of 112 Manual for SkyScan CT Analyser v 1 10 2010 10 6 Analysis of all objects in 2d Analysis Save 2D analysis results this saves in a text file the results of the two dimensional analysis of all images of a dataset inside the region of interest The values in the output text table are comma delineated each line of this table representing the results of the analysis of one image Savein fibre_sphere O 2 e g Name z Date modified Type fibre sphere 17_3dbt 6 11 2008 1 44 PM Te
104. th a single line of data corresponding to the selected binarised object Page 62 of 112 Manual for SkyScan CT Analyser v 1 10 2010 You can select one or more lines as follows Place the cursor on a line and press the left mouse button To select a range of lines left click on the first image and then left click with held down on the last line of the required range To add one line to an already chosen range or to exclude one line left click on that image with held down However the cross indicator will only light up for singly chosen objects Individual 2D object analysis aim amp xk p File name obj2b_rec_voi_0315 bmp Number of objects 167 Note Area mm 2 Perime Form Eulern Porosity Extent Orient Eccentri A 1 0 3461 3 8476 0 29 0 0 062 0 47 104 49 0 85 0 1356 0 74 0 065 0 71 20 94 0 71 0 0918 0 05 0 17 0 89 0 0592 0 07 0 33 0 97 0 0365 0 16 0 37 0 99 0 0264 0 18 0 55 0 97 0 0235 0 19 0 37 0 59 0 0224 0 20 0 36 0 97 0 0204 i 0 42 0 63 J 0 96 0 0187 j 0 17 0 0183 0 17 0 0153 0 31 0 0150 E f 0 0148 f 0 35 0 0144 0 21 nma g 0 38 0 97 0 53 i 0 79 0 98 0 93 0 63 0 95 0 54 0 76 nae naa Individual 2D object analysis a lt q amp P File name obj2b__rec_voi_0315 bmp Note Write your note here Area mm2 Perime Form f Euler n Porosity 2 Extent Orient TORREN l 0 0128 0 6828 0 35 1 0 000 0 56 8 10 0 99 PSETO Above Below Zoom In Zoom Out
105. the results file prefix ctan txt or prefix batman txt from txt to csv Then double click on the file and it will open in excel with comma delineation automatically applied 3d analysis This plug in runs 3d analysis of the ROI part of the loaded dataset 3D analysis V Basic values Additional values Total VOU volume Structure model ide Object volume Structure thickness Percent object volume Structure linear density Total VOI surhace Structure separation Object surface Stereology Intersection surface Fractal dimension Object surface volume ratio Number of objects Object surtace density Number of closed pores Fragmentation inde Porosity Lentroid Euler number Save results as test table 5 single text line C Results 106 stissue_mass thorax re stissue_d cev both text table to stdout single text line to file The configuration dialog for this plug in is the similar to that for 3d analysis at the 4 processed images page in the main body of CTAn As for 2d analysis results can be output as a single line for each dataset analysed into a commaz delineated text file containing a text table of data from multiple datasets Selecting both results in two data outputs one to the standard CTAN or BATMAN results text listing and the other to the line by line file to which the results of many analysed datasets can be added Page 91 of 112 Manual for SkyScan CT Analyser v 1 10 2010 When thickness a
106. tive value the VOI begins below the reference level The third spin box is the height of the vertical VOI in lines 300 and in the selected spatial unit e g 1 307 mm Clicking on the apply button implements the selected values to the vertical VOI Once the three reference level parameters are entered as just described the reference level itself can be changed by right clicking on a different level in the dataset window and clicking on the selection reference menu item as shown below With this action the selected dataset level becomes the new reference level with the offset and VOI height remaining as specified TA mouse_fem_5um_0815jpg CTAn File View Image Projection Region of Interest Help eam R SO Sa Bo W i g Regions of interest e a File name Al type ih mouse_ferm Sum 0618 jpg Interpolated AOI aE ih mouse_ferm Sum 061 jpg Interpolated AOI F mouse_ferm_Sum_0816 jpg Interpolated AOI it rmouise_fern Sur A145 i ateroolated Al i mouse fern 5L T Selection Reference Ctrl Insert mouse_fem 5 Set the Top of Selection Ctrl Home a mouse_fem_ot tg Set the Bottom of Selection Ctrl End F mouse_fem_5 i mouse_fem_5u Selection i Se p Animation Space 2 F mouse_fem_51 S iT mouse_fern_ Sy eh Properties Alt Enter 4h mouse_fem_Surne aucune 8 E i mouse_fern Sur 0605 jpg Interpolated AOI 8 a 4 mouse_fem_Sum_0804 jpg Interpolated ROI From the above image also please not
107. to a much smaller size with advantages for faster analysis In some special cases full size can be useful for instance where arithmetic addition or subtraction procedures are done between different datasets Page 44 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Region of interest Save saves to file the sizes types and positions of all Gg edited regions of interest and also the current vertical boundaries of the volume of interest and the current grey level thresholds in the binary page Subject to preference selection Region of interest Save new dataset from ROI saves the ROI image dey area only over the vertical range of images volume of interest as a new set of images A file save dialog opens allowing you to choose a dataset prefix and to set the colour outside the ROI area on each saved image to white or black This operation is also accessible from File Save from ROI Region of interest Cut ROI cuts the current ROI shape allowing it to be pasted to another level The current level where the cut is made ends up as y an interpolated layer Region of interest Copy ROI copies the current ROI shape allowing it to be pasted to another level The current level where the copy is made remains unchanged Region of interest Paste ROI pastes a previously cut or copied ROI shape to the current dataset level Edit polygonal ROI Alternates between an ROI boundary showing corner dots for editing mo
108. ton In the Status bar at the right the relative displacement ROI offset of the ROI shape will be displayed lf you start drawing a freehand shape with the left mouse button held down in the field of a crossection image on the ROI page the polygonal ROI type is automatically set A line bounding the new ROI will appear At release of the button the figure will be closed The drawn line has small square markers at the polygonal corners as shown in the image above These corner markers can be moved by left mouse button drag and drop allowing editing of the drawn shape see below Nodes can also be individually inserted moved and removed Page 42 of 112 Manual for SkyScan CT Analyser v 1 10 2010 lf you begin such drawing on an image with an interpolated region of interest the ROI type will change to polygonal Where interpolated image levels exist any modification of the size position or shape of the ROI of any image will call a re computation of all interpolated images between the image with the modified ROI and the next images with an edited ROI above or below this image Note that interpolated images are shown as yellow icons and polygonal edited images as red For control of the region of interest use these commands Region of interest Expand stretches the active fixed region of interest up to the size of the crossection image Region of interest Copy to All copies the active region of interest to all images
109. urface to bone volume ratio CTAn gives two options for the set of morphometric parameter names 1 General scientific parameter names and 2 parameter names compliant with ASBMR histomorphometry nomenclature Make your choice in the preference setting general nomenclature Brightness The intensity or brightness of x rays striking elements of the x ray camera Projection x ray images are shadow images where objects with differing x ray absorption in the x ray path are imaged as differing brightness values across the camera detector elements low brightness implies high absorption of the x ray path reaching that detector element and vice versa By the algorithm of Feldkamp cone beam reconstruction shadow projection images are translated into crossectional images where pixel values also indicate brightness In crossection images high brightness equals low x ray density opacity and vice versa Page 108 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Caching Optional copying of a loaded dataset to a local temporary file The locating of each image file by the computer on loading into CTAn takes time and therefore when the dataset size is large or the dataset is loaded from a remote drive across a network the time taken to load image files can become significant If you have enough free space on the hard disk you can reduce this time by activating a caching option after which the files will be read only once into the tempora
110. ustom processing or BatMan always use ROI datasets with reduced size Custom processing has a higher memory demand than the main body of CTAn and thus minimizing dataset size will facilitate operations in custom processing and BatMan Page 46 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Saving a new ROI dataset creates a much smaller dataset which results in faster calculation and image processing of the same VOI especially in custom processing or BatMan Save in di mouse_fem_13mp_trabecular E a EF ue Name Date modif Type Size This folder is ernpty File name mouse fem_13mp trabecular Save as type BMP files bmp Background ae Rotate by The dialog box for saving an ROI dataset includes the option to rotate the saved images in the horizontal plane around a central vertical axis with the associated option of smoothing to minimize angular resampling artifacts 8 2 The reference level ROI tool In some applications the vertical range of the volume of interest VOI i e the upper and lower limits of the selected range of image levels is specified with reference to a fixed object or feature in the scanned dataset An example is in bone biology where a bone like a rodent femur is scanned at the knee distal end Close to the knee is the femur s growth plate made of cartilage and usually trabecular spongy bone is selected for analysis at the distal femur starting a small fixe
111. ve add remove and a smooth boundary with four corner markers for resizing and reshaping the polygon as a whole te ee Note Under the help menu a Keyboard Shortcuts window can be opened also by pressing Alt F1 listing all the available keyboard shortcuts to CTAn functions R What s This Help Topics Fl Keyboard Shortcuts Alt F1 W About CTAn Page 45 of 112 Manual for SkyScan CT Analyser v 1 10 2010 The edit polygonal ROI button alternates between a mode in which the whole shape can be edited by moving corner markers by mouse drag and drop left image as for other fixed ROI shapes and a mode in which all polygon boundary corners can be moved added or removed right image 8 1 The save new dataset from ROI function Special emphasis should be given to the save new dataset from ROI function since using this function confers several important advantages and can make analysis quicker and easier Once ROls are set over a selected range of slices giving the volume of interest VOI the new dataset thus created contains only the part of each image within the ROI over the selected VOI range only see the two images below Note in the preferences ROI page under the heading Save images the option to accumulated ROI bounds should be checked in order for the created ROI dataset to be cropped to the minimum size NOTE ON CUSTOM PROCESSING When analysing datasets in c
112. vesiontta OK YOCAN The user s guide Contents 1 Introduction 3 2 First start up of the program 4 3 Set up of preferences 7 4 Opening files 8 4 1 Conversion of different image formats at opening 12 4 2 Crossection image window 15 4 3 Dataset bar 19 4 4 Shadow projection bar 20 4 5 Palette bar 23 5 Image viewing modes summary 24 6 Volume model real time viewing 26 6 1 Before you start hardware requirement graphics card 26 6 2 Launching volume modeling 27 7 Page 1 Raw images 31 7 1 Profile bar 32 7 2 The Maximum Intensity Projection MIP 34 7 3 Protractor tool 3 7 4 The hand measurement tool 3 8 Page 2 Region of interest 41 8 1 The save new dataset from ROI function 46 8 2 The reference level ROI tool 47 9 Page 3 Binary images 50 9 1 Histogram bar 50 9 2 BMD calibration by the histogram tab in preferences 53 9 3 Modes of image view at the binary page 99 9 4 File menu items at the histogram page 99 10 Page 4 Morphometry 59 10 1 Analysis bar 59 10 2 Commands of the analysis menu 59 10 3 Individual object analysis in 2D 62 10 4 Individual object analysis in 3D 64 Manual for SkyScan CT Analyser v 1 10 2010 10 5 Analysis of all objects in 3D 65 10 6 Analysis of all objects in 2D 72 11 Page 5 Custom processing 73 11 1 Plug ins bar 74 11 2 Batch processing mode 17 12 The printed report 82 References 85 Appendix A Description of plug ins in custom processing 86 Appendix B Fo
113. viewing after the execution of a single plug in or list of plug ins Page 75 of 112 Manual for SkyScan CT Analyser v 1 10 2010 In the Plug Ins bar there are commands which become active in some tabs and are disabled in others Restore dataset restores a duplicate of the dataset images reversing the previous image modifications This command becomes active after images are modified Run plug ins starts execution of a single selected plug in when the tab Internal or External is active and executes a list of plug ins when the tab Task list is active IN Add plug in to task list adds a selected plug in in the Internal or External tab to the task list in the Task list tab Move plug in down shifts a selected plug in down by one line on the list changing the sequence of execution of plug ins in the Task list tab Move plug in up shifts a selected plug in up by one line on the list t changing the sequence of execution of plug ins in the Task list tab Delete plug in deletes the selected plug in from the list of the Task list x tab Import task list reads from the disk ctt file a list of plug ins and shows them on the Task list tab Export task list saves on disk cit file the list of plug ins shown on the Task list tab Plug in configuration shows the configuration dialog of the selected plug 4 When you add any plug in to a list on the Task list tab it is copied with its curr
114. ween linear and logarithmic Calibration Implements density EEEE T p calibration in the Hounsfield Unit and attenuation coefficient scales Index means grayscale Enter measured calibration values in the corresponding boxes and then press OK Auto normalises to maximum range 0 255 Evaluate on re opening the window Calibration unit Min value Max value 259 Histogram From Image shows the histogram distribution of brightness ana from the whole area of the current image only Histogram From Selection shows the histogram distribution of brightness from the whole area of all images of the dataset Histogram From Dataset shows the histogram distribution of brightness ee from the whole area of all images of the dataset Grayscale indexes Sets the displayed density scale to units of grayscale Grayscale is referred to as index Hounsfield Units Sets the displayed density scale to units of Hounsfield units Bone Mineral Density Sets the displayed density scale to units of Bone Mineral Density BMD in g cm calcium hydroxy apatite Attenuation coefficient Sets the displayed density scale to units of attenuation coefficient p according to I Ie Histogram Halftone view displays the original grey level image with green highlighting with the binarised part of the image superimposed in red Page 52 of 112 Manual for SkyScan CT Analyser v 1 10 2010 Histo
115. x will appear asking you to enter your personal data and the identification number of the program which you recorded at the initial opening of the downloaded CTAn program g Save your personal data and identification number they will be necessary when the program checks your license or if you install CTAn on another PC You can find the identification number of the program Product ID and the version in the dialog Help About CTAn Page 4 of 112 Manual for SkyScan CT Analyser v 1 10 2010 About CTAn CT Analyser Version 8 8 8 8 Copyright 2003 08 Skyscan Web wwwseskyscan be E mail info skyscan be Product ID 666491DB6 5D41 4E06 9684 666491DBS4C3 Licensed to Phil Salmon Downloaded updates to CTAn and CTVol require no additional licensing just overwrite your CTAn exe file in the same directory as the lic license file Also note after licensing the program the product ID displayed in the about window is not the same as the original program ID so it can t be used to install CTAn on other PCs you need the original ID number for this The latest version of the program is available for download at the address http Awww skyscan be products downloads htm 2 1 The licensing of different user profiles The application of the CTAn license requires administrator rights in Windows However the normal operation of CTAn once licensed does not require administrator rights The run as
116. xt Document fibre_sphere_ 3d 6 11 2008 1 26 PM Text Document Filename fibre_sphere_17__2d bt Save as type Tet files bd Append to file Note on text report files when prompted to enter a filename for a report text file the default file extension will be txt For instance object_3d txt or object_2d txt The output file will be an ASCII text file However you can optionally change the extension of the report file to csv This stands for comma separated values and is a format recognised by Microsoft Excel The file created will be the same ASCII text file but it can be easily and quickly opened in Microsoft Excel by double clicking side stepping the Excel text import wizard lt is possible to display or to hide the Analysis bar with the menu E View Analysis Page 72 of 112 Manual for SkyScan CT Analyser v 1 10 2010 11 Page 5 Custom processing The custom processing page represents a different way of working with CTAn The analysis functions from the previous CTAn pages binarisation 2d and 3d analysis etc can be used in custom processing together with many additional functions such as image processing operations e g smoothing despeckle Operations that you choose to run are executed in a task list that you can build and configure Combinations of the available operations can allow a very wide range of 3d image analysis functions to be achieved When you select the 5 custom process
117. y images density analysis and 3d model building View Processed images 3d and 2d morphometric analysis Alt 1 4 viewing of analysed images and calculation results View Custom processing a user interface for image processing Alth 5 and analysis tasks as sequential plug ins viewing of resultant E images After switching to one of these modes a corresponding tab appears on the Dataset bar These tabs also can be used for switching between viewing modes Please note that the ALT 1 5 keyboard shortcuts for jumping between the five CTAn pages are a useful way to move around in CTAn between the pages for instance when selecting a binary threshold value at the binary page where you need to compare the binarised image at page 3 with the original grey scale image at page 1 In the following five chapters the five pages of CTAn will be described in detail Page 25 of 112 Manual for SkyScan CT Analyser v 1 10 2010 6 Real time volume model viewing 6 1 Before you start two quick hardware checks before you begin volume modeling in CTAn These preliminary actions are advisable before using both SkyScan software products employing volume modeling CT Analyser and CT Volume 1 Goto the control panel of Windows to system and device manager Select display adaptors Read your type of graphics card for example NVidia FX or GeForce Then go to the web site of the manufacturer of th

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