CTAn UserManual

SkyScan CT-Analyser (“CTAn”)
User Manual
CTAn User Manual 1.20 Jan / 2020 0

© Bruker microCT 2020
CTAn was created by Bruker microCT in Belgium
Kartuizersweg 3B
2550 Kontich
Belgium

1. Contents
1. Contents .............................................................................................................. 2
2. Introduction.......................................................................................................... 7
3. First start-up of the program ................................................................................ 8
3.1. The licensing of different user profiles .......................................................... 9
3.2. Co-licensing of the 3D viewing program ANT and CTAn upgrades requiring
re-authentication ............................................................................................... 11
3.2.1. Licensing of ANT with CTAn ............................................................... 11
3.2.2. Upgrades requiring license re-authentication ...................................... 11
4. Set-up of preferences ........................................................................................ 12

4.1. Introduction to preferences ......................................................................... 12
4.2. Brief description of the preference tabs ...................................................... 12
4.2.1. Preference tabs: introduction .............................................................. 12
4.2.2. Keyboard shortcuts in CT-Analyser..................................................... 15
5. Import and export of image files ........................................................................ 16

5.1. Import of image files ................................................................................... 16
5.1.1. Conversion of different image formats at opening ............................... 21
5.2. Export of image files ................................................................................... 25
5.2.1. Export to AVI movie file ....................................................................... 25
5.2.2. Export to for mobile devices: I3M for Apple and V3X for Android ........ 27
6. The seven part structure of CT-Analyser: summary .......................................... 28

6.1. The panes of the CTAn program window ................................................... 30
6.1.1. The volume rendering pane ................................................................ 31
6.1.2. The shadow projection pane ............................................................... 31
6.1.3. The dataset pane ................................................................................ 33
6.1.4. The cross-section image pane ............................................................ 35
6.1.5. The palette and analysis pane ............................................................ 38

7. Real time volume model viewing ....................................................................... 40
7.1. Before you start – two quick hardware checks before you begin volume
modeling in CTAn ............................................................................................. 40
7.2. Launching volume modeling ....................................................................... 42
7.2.1. The volume modelling buttons from right to left:.................................. 43
8. First Page: Raw Images .................................................................................... 47

8.1. The profile bar (with MIP and other imaging functions) .............................. 47
8.1.1. Save profile ......................................................................................... 48
8.1.2. Single section reslicing ........................................................................ 48
8.1.3. Multiple cross-section reslicing............................................................ 49
8.1.4. The maximum intensity projection (MIP) ............................................. 51
8.1.5. The ruler and protractor tool ................................................................ 55
8.2. The hand measurement tool ...................................................................... 57
8.2.1. Angle measurement with the manual “measure” tool: ......................... 57
8.2.2. Line measurement with the manual “measure” tool ............................ 57
8.2.3. Path measurement with the manual “measure” tool ............................ 58
8.2.4. Coordinate measurement with the manual “measure” tool: ................. 58
8.2.5. Measure tool function buttons ............................................................. 59
9. Second Page: Region of interest ....................................................................... 60

9.1. A note on terminology ................................................................................ 60
9.1.1. This is the row of function buttons at the ROI page: ............................ 60
9.2. The “save new dataset from ROI” function ................................................. 64
9.2.1. Note on custom processing: ................................................................ 64
9.2.2. The dialog box for saving an ROI dataset includes these items .......... 66
9.3. The reference level ROI tool ...................................................................... 67
9.4. Drawing multiple ROI shapes, and cutting subtractive regions .................. 68
9.4.1. Adding additional ROI shapes ............................................................. 69

9.4.2. Removing or subtracting from an ROI shape ...................................... 70
10. Third Page: Binary selection.............................................................................. 71

10.1. Histogram bar ............................................................................................. 71
10.1.1. Commands of the Histogram menu: .................................................... 73
10.2. BMD calibration by the histogram tab in preferences ................................. 74
10.3. Modes of image view at the binary page: ................................................... 76
10.4. File menu items at the histogram page ...................................................... 76
10.4.1. The Locality and tolerance parameters for adaptive rendered 3D

models ........................................................................................................... 78
11. Fourth Page: Morphometry................................................................................ 79

11.1. The Analysis bar......................................................................................... 79
11.1.1. Commands of the Analysis menu:....................................................... 79
11.2. Individual object analysis in 2d: .................................................................. 82
11.3. Individual object analysis in 3d: .................................................................. 84
11.4. Analysis of all objects in 3d ........................................................................ 86
11.4.1. Single line text output for automatic creation of table of results from
multiple datasets ............................................................................................ 89
11.4.2. Mean intercept length analysis (pane in Advanced preferences tab) .. 89
11.4.3. Advanced options for 3D morphometric calculations .......................... 90
11.5. Analysis of all objects in 2d ........................................................................ 92
12. Fifth Page: Custom processing ......................................................................... 93

12.1. The Plug-Ins bar ......................................................................................... 95
12.1.1. The Plug-Ins bar has the following five tabs ........................................ 95
12.1.2. The button bar in the Custom Processing page .................................. 96
12.2. “BatMan” – the batch manager for automation ........................................... 98
12.2.1. The Task List has three columns relating to each selected task: ...... 100
12.2.2. The Dataset list has five columns relating to each selected dataset: 101

12.2.3. Preferences in BatMan ...................................................................... 101
13. The printed report ............................................................................................ 102

14. References ...................................................................................................... 105
15. Appendix A: Description of plug-ins in custom processing ........................... 106
15.1. Thresholding ............................................................................................ 108
15.1.1. Adaptive thresholding ........................................................................ 109
15.1.2. Otsu and Ridler-Calvard thresholding ............................................... 110
15.1.3. Other automatic statistical methods and hysteresis thresholding ...... 112
15.2. Save bitmaps ........................................................................................... 112
15.3. 2d analysis ............................................................................................... 114
15.4. 3d analysis ............................................................................................... 115
15.5. Filtering .................................................................................................... 116
15.5.1. The Unsharp mask ............................................................................ 117
15.5.2. Conditional mean .............................................................................. 118
15.5.3. Contrast stretching ............................................................................ 118
15.5.4. Contrast enhancement ...................................................................... 119
15.5.5. Anisotropic diffusion filtering.............................................................. 120
15.6. Morphological operations ......................................................................... 121
15.7. Despeckle ................................................................................................ 123
15.7.1. The RANGE despeckle option .......................................................... 124
15.8. 3D model .................................................................................................. 125
15.8.1. Algorithm options for surface-rendered 3D models: .......................... 125
15.9. Shrink-wrap ROI ....................................................................................... 126
15.9.1. The other shrink-wrap options: .......................................................... 128
15.10. Reload ...................................................................................................... 130
15.11. Histogram ................................................................................................. 130
15.12. Individual object analysis .......................................................................... 131

15.12.1. Individual 2D object analysis ............................................................. 131
15.12.2. Individual 3D object analysis ............................................................. 133
15.13. Bitwise operations .................................................................................... 135
15.14. Arithmetic operations................................................................................ 136
15.15. Geometric transformations ....................................................................... 138
15.15.1. The five geometric transformations are: ............................................ 138
15.16. Comment .................................................................................................. 138
15.17. Primitive ROI ............................................................................................ 139
15.18. Local orientation ....................................................................................... 141
15.18.1. Binary masking of objects prior to running Local Orientation: ........... 142
15.19. Compositing ............................................................................................. 143
16. Appendix B. Boolean image operations........................................................... 146

17. Appendix C: Format of the CTAn command line ............................................. 150
17.1. Examples of use: auto-analysis following NRecon ................................... 151
18. Appendix C: Glossary of terms used in the CT-Analyser manual .................... 153

2. Introduction
CT-Analyser (CTAn) is an application for measuring quantitative parameters and constructing visual
models from scanned 3D datasets obtained with SkyScan microCT instruments.
It can also be used for 3D and 2D images obtained from other imaging modalities. To this end, CTAn
is able to import a wide range of 3D image formats, including DICOM datasets.
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. A global threshold
can be selected automatically by the Otsu method [1], either single or multi-level. 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 microCT scan datasets. Reporting of data is flexible – including spreadsheet
(e.g. Excel) ready data table output, and suited to the requirements of high throughput analysis.
Raw images
Region of interest
Binary selection
Morphometry
Custom processing
CT-Analyser is organised into five stages as shown, for optimal and intuitive work-flow.

3. First start-up of the program
The program does not require special installation on the computer, it runs from the single
“CTAn.exe” file in a directory on the hard disk or a network drive. The first start-up should be under a
user profile with administrator rights, to allow licensing. 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 currently installed by the user, the program can work in one of the following modes:
• demonstration mode, established by default, in which some functionalities are disconnected;
• limited (30-day's full functionality of the current version of the program);
• unlimited.
To obtain a limited or full license it is necessary to register the program at Bruker-microCT; to do this,
email to info@bruker-microct.com the following personal data:
• the name of the user;
• the title of the organization;
• 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 Bruker-microCT. 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 CTAn a dialog box
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.
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.
Furthermore, a separate document is available from Bruker-microCT titled “How to license CT-
Analyser” with detailed explanation of the licensing process.

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://www.Bruker-
microCT.be/products/downloads.htm
3.1. The licensing of different user profiles

The application of the CTAn license requires administrator rights in Windows. In the current CTAn
versions since version 1.10.4 the user is prompted to allow acquisition of administrator rights by the
program when needed. However in earlier versions of CTAn, licensing might require the program to
be “run as administrator” using the right-click option (see image below).
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:

If 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 Bruker-microCT web site in the link group for CTAn and CTVol.
It is possible to set a desktop shortcut icon to CTAn to run in administrator mode. To do this in
Windows 10, right-click on the icon and select “Properties”.
Then click “Advanced”. In the new window that opens,

the option to run CTAn automatically as administrator
will be selectable:

3.2. Co-licensing of the 3D viewing program ANT and
CTAn upgrades requiring re-authentication
3.2.1. Licensing of ANT with CTAn

To run the ANT 3d visualisation program using the same electronic license as CTAn, please update it
to version 2.4.2.0 or higher, and place the “ant.exe” file in the same directory as “ctan.exe” and the
license file “ctan.lic”.
3.2.2. Upgrades requiring license re-authentication

In the history of development 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. This upgrade was in 2006.

4. Set-up of preferences
4.1. Introduction to preferences
Under the file menu there is the “preferences” item for CTAn.
This allows you to set preferences relating to a number of the
program’s operations, calculations and data output formats. It is
divided into eight tabs:
In this chapter the first, “general” tab will be described in detail.
The remaining tabs refer to functions covered in the forthcoming
chapters, so they are dealt with in turn in, each in its
corresponding chapter.
4.2. Brief description of the preference tabs
4.2.1. Preference tabs: introduction

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.
Animation: This tab allows you to adjust the speed of animation both for display (visualisation) and
for exported avi movie files.
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).
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).
Volume: This tab has options concerning the resolution level of real time volume modelling in CTAn,
which are constrained by the computer’s video graphics card (see chapter 6).
Tools: In this tab you enter the directory path to the Bruker-microCT CTVol program to allow it to
automatically open on creation of a 3D model file.

Directories: In this tab you can specify the directory path to a temporary file (required by CTAn, a
default temp file is specified automatically) and or external plug-ins for custom processing (see
chapter 11).
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).
The “general” tab of preferences
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. Bone ASBMR
nomenclature follows the recommendations of the ASBMR committee on histomorphometry
nomenclature (Parfitt et al. 1987) and is appropriate for study of trabecular bone. For other
applications the “general scientific” nomenclature is more appropriate.
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, millimetres, 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.
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.
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: Cross-section 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).
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”).
Filename postfix length: Bruker-microCT

datasets can have either 4 or 8 digits in the
cross-section image filename postfix number.
Other non-Bruker 3d datasets can have
different numbers of digits in their postfix
number (e.g. various Dicom types). To allow
datasets with different numbers of postfix
digits to be imported into CTAn, the postfix
length can be changed in preferences, with an
“Auto” option for auto-detection of the
number of postfix digits.
Show position inside image: Checking this tick

box activates the mode in which the mouse
cursor, when over the projection or cross-
section images, will have its position
coordinates relative to the origin shown in a tool tip (in the selected units of measurement) – as
shown to the right.
Raw data file type: Enter here the filename extension of a non-Bruker-microCT image format that
you wish to import into CTAn – see section 4.1.

Forward mouse wheel to controls: Volume rendering in CTAn: with this option checked, the mouse
wheel can be used to move a 3d volume rendered model closer or further away in the volume
rendering window (see section 6, page 28).
4.2.2. Keyboard shortcuts in CT-Analyser

From the help menu and also by pressing ALT+F1, a full
listing of available key-board shortcuts in CTAn is
displayed. These are useful for jumping between display
pages and speeding up repetitive operations.

5. Import and export of image files
5.1. Import of image files
The program can load eight types of files (BMP, JPG, PNG, TIFF, RAW, ISQ, DICOM and VFF), 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 (.bmp extension).
JPG-files: all jpg types are loadable for viewing, but for analysis only eight-bit grayscale images
will be processed (.jpg extension).
PNG-files: all png types are loadable for viewing, but for analysis only eight-bit grayscale images
will be processed (.png extension).
TIFF-files: for viewing and analysis the program supports sixteen bit tiff grayscale images
created by Bruker-microCT instruments and software (.tif extension).
RAW data: this is a “wildcard” format that allows any image format to be imported – you will
need to enter image file parameters, as explained a little later in section 4.1. (extension entered by
user).
ISQ-files: ISQ is the format created by Scanco Medical AG microCT scanners, and can be read
directly into CTAn (.isq extension).
DICOM-files: Dicom files can be directly loaded into CTAn (of the multi-slice type with .dcm
extension).
VFF-files: This format was used by GE locus microCT systems
Other image formats, including from equipment other than Bruker-microCT, can be opened in CTAn –
please refer to section 4.1 below.
Colour images
Images in BMP, PNG or JPG with RGB colour 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 tiff-files, a dialog is opened which transforms the image data to 8-bit for
analysis within CTAn. A brightness 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.
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.
The button Apply 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 files 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 А). 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 File / Open…. Ctrl + O ,
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 in a 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.
Suffix length: after “open as”, there is a # followed by a box displaying the number of digits in the
filename suffix. For SkyScan datasets this is 4 by default, e.g. the in filename

samplescan_rec0001.bmp the final number has 4 digits. This number can be changed allowing for
example non-SkyScan 3D image formats to be loaded. (Note also that large datasets from SkyScan
systems can also output filenames with a suffix up to 8 digits.)
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 (222). This allows faster manipulation, morphometric measurement and model
building at lower spatial resolution. The factor of diminution is from 2 to 16 by length (8 to 4096 by
volume).
Under the resize option is the connected option of “2D” or “3D”. 3D resizing includes resizing in the Z
depth axis, while with 2D resizing, pixels are binned in the 2D XY plane only and redundant cross-
sections are discarded. 3D resizing is recommended for better resulting image quality.
 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.

This caching begins to work with the next opening of a dataset, so if a dataset is already
open when you select caching, reload it.
 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 the button ... .
In the opened dialog box, specify a path and folder and press the button OK .
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.

5.1.1. Conversion of different image formats at opening
Micro-CT or other 3D image datasets from other, non-Bruker-microCT sources and equipment can be
loaded into CTAn, which has a flexible interface for accepting and importing such datasets. Two items
in the “general” tab under the preferences relate to the import of different file types. They are
shown by the red boxes in the preferences screen copy below.
RGB to grey: this item provides options for converting colour images with RGB (red-green-blue)
image data to grey format. Only grey format images can be analysed in
CTAn.
The options for colour to grey conversion are:
• No: no conversion
• Luminance: this calculates the grey pixel value from a weighted
balance of the RGB values according to the ratio R:G:B – 0.2126 :
0.7152 : 0.0722.
• Red channel: takes the grey value as the red channel value only
• Green channel: takes the grey value as the green channel value only
• Blue channel: takes the grey value as the blue channel value only
Raw date file type: raw.

Datasets in non-Bruker-microCT formats can be imported into CTAn under the specification of “RAW”
file. This is a flexible designation that can be assigned to various non-Bruker-microCT formats. The
specified non-Bruker-microCT format can be selected as “RAW” on opening a dataset, as shown in
the image below.
The raw data file (RDF) can be a single volume or a multiple volume.
5.1.1.1. Example: loading images of a hypothetical external format .XYZ
First, in preferences / general, the Raw data file type is changed from “raw” to “xyz”:
Then load the .XYZ files with the usual load images dialog:
Note: after “open as” there is a # symbol followed by a box in which you can enter the suffix length –
the number of digits at the end of each cross-section filename denoting cross-section level in the Z
axis. Datasets with other than 4 suffix digits can be loaded.
For a multiple volume RDF the information about Z position is taken from suffix number.
On clicking open, the dialog shown below will appear requiring input of the image format parameters
“XYZ” format:

On loading a non-Bruker-microCT 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:
• Data type (integer, floating point, etc.)
• Byte order (little endian (WIN) / big endian (MAC) see the Wikipedia entry:
http://en.wikipedia.org/wiki/Endianness
• Scan order: is the first image bottom or top in the Z axis?
• Header size, in bytes
• Pixel size, in microns
• Image width and height (pixels)
• “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 minimum and maximum must be specified.
• 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 <= n < Z size).
5.1.1.2. Command line opening of CTAn with options (arguments)

CTAn can be run from the Windows command line. As well as directly from Windows command line,
this includes in the preference page in SkyScan NRecon, to set up automatic opening of
CTAn/BatMan after reconstruction, or in the properties of a desktop shortcut icon for CTAn.
To see all the command (/letter) options, first go to Windows command line
by entering “cmd” in the search window, bottom left on the Windows
screen.
Then enter the commands:

c: Go to the C: drive
cd skyscan Go to the SKYSCAN directory
ctan/? Open a window showing CTAn command line options

This window will open:
The above window lists the options, or “arguments”, that can be added to the opening of CTAn.
These include the running in BatMan mode, loading a .ROI file, loading another dataset into the
CLIPBOARD, loading of a task list, and downsizing to a lower resolution by voxel binning – referred to
above as “decrease images”.
It is also possible to set a task list in BatMan mode to run automatically after opening with /A.

5.2. Export of image files
5.2.1. Export to AVI movie file

The currently opened stack of image files can be exported as an AVI movie file. Under the file menu,
select “export” and two options appear: ‘to movie file” and “to mobile device”.
Note that any image stack that is loaded into CTAn can be made into a movie in this way. This
includes image stacks with RGB colour information and other non-SkyScan dataset formats. For
instance, image stacks created from the flight recorder (movie maker) in both SkyScan CTAn and
CTVol can be made into an AVI movie in this way. However for RGB images the further analysis
functions in CTAn are not available.
Selecting “to movie file”, a save file dialog will appear for you to save an AVI file:
There is an option tick-box at the bottom of the save AVI window allowing your PC’s default AVI
player – such as Windows Media Player – to automatically display the AVI movie once saving is
complete.

When you click “save”, another dialog will appear with AVI compression options:
The default (what happens when you do nothing) will be “full frames (uncompressed)” which can
result in very large files. We would recommend the Microsoft Video 1 codec, a reliable compressor
which has the advantage of being present on all Windows PCs. Some compressors such as Windows
Video 1 require a value for compression to be set with a slider:
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.

5.2.2. Export to for mobile devices: I3M for Apple and V3X for Android
The second export option is export for mobile devices. In the “Save as type” drop menu are two
choices: i3m for Apple and vxm for Android:
I3M is the 3d file format employed by “ImageVis3D Mobile”, a

volume rendering app intended for Apple smart devices (iPad,
iPhone and iPod Touch.) It is freely available through the Apple
App Store. The file created by the “export to I3M” command is a
single file for volume data (up to 8 MB in size), with the .i3m
extension.
VXM is the 3d file format used by
Please refer to the SkyScan document “CTVox Quick Start Guide”

for more details about the ImageVis3D Mobile application and its
use with SkyScan generated 3D models.

6. The seven part 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 also
has seven parts, which appear as separate windows, and which correspond to the normal sequence
of steps through the analysis process; or the “workflow”. Here these seven parts:
1. The raw image page

2. The Region of interest page
3. The Binary image page
4. The Morphometry page
5. The Custom Processing page
6. The Clipboard
7. The volume rendering window
Separating these functions into pages reduces the complexity and clutter (number of buttons and
objects) on each window of the program, improving the user-friendliness of the program interface.
On opening a dataset, the first six of these steps or pages become accessible as indicated by the
appearance of buttons under the menu bar.
These six pages are also listed under the “view” menu:

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);
Alt + 1 ,
View / Raw images – Initial viewing of images, profile and longitudinal resampling;
View / Region of interest – Selection and viewing of regions of interest (ROI) of Alt + 2 ,
images, saving the ROI dataset;
View / Binary selection – Selection of the binary thresholds and viewing of Alt + 3 ,
resultant binary images, density analysis and 3d model building;
View / Morphometry – 3d and 2d morphometric analysis, viewing of analysed Alt + 4 ,

images and calculation results;
View / Custom processing – a user interface for image processing and analysis Alt + 5 ,
tasks as sequential “plug-ins”, viewing of resultant images
View / Clipboard – the clipboard is an additional image channel in which the Alt + 6 ,
original or a transformed (e.g. binarised, processed) copy of the loaded dataset can
be stored.
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+1-6 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.
6.1. The panes of the CTAn program window

The program window of CTAn is shown below. It is divided into a four “panes”, or bounded sub-
regions, shown in red squares, which will be briefly described. Following this, there is an introduction
to the file / preferences option in CTAn.
1 2 3
4 5
The five program panes are:

1. The volume rendering pane
2. The shadow projection pane
3. The dataset pane
4. The cross-section image pane
5. The colour palette and analysis pane
These will be described in turn.

6.1.1. The volume rendering pane
The volume rendering pane and creation and viewing of volume models, as well as maximum
intensity projection (MIP) images, is described below fully, in chapter 6.
6.1.2. The shadow projection pane
In datasets of images created by Bruker-microCT 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 pane, and simultaneously in the menu there is a new submenu Projection, which
is also accessible by right button click on the projection image.
6.1.2.1. Commands of the menu Projection:

The right mouse-click drop menu in the projection window is divided into three parts by horizontal
lines. The upper part has three “show” items connected with how much of the projection is
displayed:
• Show full area – shows the whole projection image without any modifications;
• Show active area – shows only the part of the projection image for which cross-sections are
present in the dataset;
• Show selected area - shows only the part of the projection image corresponding to the
current vertical selection of cross-sectional levels – if this selection is restricted, the
projection image becomes correspondingly restricted and magnified.

The second part of the projection menu has items controlling the highlighting in green of parts of the
projection image:
• Disable highlighting – no part of the projection image will be green-highlighted

• Highlight inactive area – highlights in green cross-sections which are present in the
projection image (as horizontal pixel lines at the top and bottom of the projection) but for
which no cross-sections are present in the open dataset – these are called “inactive” areas.
• Highlight non-selected area – highlights in green cross-section excluded from the vertical
volume of interest (VOI) selection, as well as inactive areas.
The third and bottom part of the projection menu allows selection or de-selection of the vertical and
horizontal rulers at the right and bottom margins respectively of the projection image:
• Show vertical ruler – shows or hides the vertical ruler.

• Show horizontal ruler – shows or hides the horizontal ruler.
The red line inside the projection image indicates the position of the displayed cross-section image in
the dataset. If you double click the left mouse button at a location on the projection image, the
cross-section 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 the projection image and the active cross-section 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 menu
View / Shadow projection.
6.1.3. The dataset pane
For switching between cross-section images there is the Dataset pane, on which a list of the loaded
dataset image files is displayed. For moving up and down the list you can use the keys ↑ , ↓ or
the slider located to the left of the dataset bar.
Right-clicking in the list box on a particular cross-section image number causes a drop-menu to
appear which offers the following functions:
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.)
Clicking on this option sets the current image level as the

top of the selected VOI range.
Clicking on this option sets the current image level as the

bottom of the selected VOI range.
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.
Starts and stops animation through the cross-sections

within the selected VOI range.
Displays the image properties including directory path.
To the right of the list there are two sliders (shown in red circles) 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:
The top, bottom and middle line are indicated, in both line number and height.
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 cross-section 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-VOI images.

It is possible to display or to hide the Dataset bar from the menu View / Dataset.
6.1.4. The cross-section image pane
When the loading of images is complete, the program will show on screen a cross-section image
(below). In the menu bar a new submenu Image will appear, which contains commands for control of
the cross-section image display pane. These commands can also be accessed by pressing the right
mouse button (right-clicking) in the cross-section image field.
Please note: in order for the keyboard commands listed below to operate on the cross-section
images (moving up and down levels for instance) it is necessary that either the dataset bar (top left
window listing all image levels) or the cross-section image window (bottom right) are active. To make
a window “active” just click on it (left mouse).
Commands of the menu Image:
View the above image ↑ , mouse wheel up
View the below image ↓ , mouse wheel down
Enter a chosen zoom value Shift + mouse wheel ↑↓
Increase image magnification Shift + mouse wheel ↑

Decrease image magnification Shift + mouse wheel ↓
Fit image to window (note – window size * on number pad

can be adjusted)
Set image to actual size (image pixel = “=” key

display pixel)
Opens the manual measurement tool. Opens a tool for manual

measurement of distances angles,
with saving of results to a text file.
Go to hand mode In hand mode you can move the

image position using left mouse
button drag-and-drop.
Deselect hand mode
From the menu item File / Preferences… you can set the upper value of frequency of image
animation:
This animation speed cannot always be realised. With very large sized images memory will become
limiting and the speed will become less than indicated.

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.)
If 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 right arrow key
You can change the magnification of the displayed cross-section 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 left 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.
There is a hand icon button at the right of the upper menu bar. Pressing this makes a hand
icon appear in the cross-section 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 cross-section image viewing window.) Pressing the
hand button a second time makes it disappear and restores the default arrow cursor.

6.1.5. The palette and analysis pane
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.
Colour palette with the “colour density range” slider selected in preferences / tools.
Colour palette with the “brightness / contrast” slider selected in preferences / tools.
Images can be inverted by clicking on the “Yin-Yang” icon, set to one of four pallets (original,
half-tone and two colours). 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 palette slider.
In CTAn preferences / tools you can choose between “brightness / contrast” and “colour density
range” sliders for the colour palette. Usually the “colour density range” gives an easier adjustment of
the correspondence of colour and brightness values with image grey scale.
You can display or hide the Palette bar from the menu View / Palette.

Under “palette window sliders” there are two choices of control mode – “colour density range” is
usually more convenient for adjusting grey values or colours of displayed images.
6.1.5.1. Limiting colour palette selection to selected CTAn pages
At the lower right of every page window, there is a selection box allowing you to make tick-box
selections as to which CTAn pages are affected – or not affected – by the colour palette selection.
The option “volume” refers to the volume rendering viewing window at the “Raw images” page.

7. Real time volume model viewing
7.1. Before you start – two quick hardware checks
before you begin volume modeling in CTAn
These preliminary actions are advisable before using both Bruker-microCT software products
employing volume modelling – CT-Analyser and CT-Voxel (“CTVox”).
1. Go to the control panel of Windows, to “system” and “device manager”. Select “display
adaptors”. Read your type of graphics card – for example NVidia Quadro or GeForce (GTX) or Tesla.
Then go to the web site of the manufacturer of the 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. Go to 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 CTVox the same information is visible
under options / preferences /
It is suggested that you first set it to 768 (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 modelling, try the higher available resolutions. Note that with 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 CTVox (Open GL 2); in such cases the volume modelling 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 modelling in CTAn / CTVox cannot divide its
memory requirement into halves, thus in such a case only half the memory is available.
Find out by experimentation the resolution level that gives an acceptable image quality combined
with control responsiveness.

7.2. Launching volume modeling
The top button shown below circled in red launches the volume modelling:
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.
With the volume modelling 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. Non-selected 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 colour.
Both left and right mouse button drag and drop are used to control the models position:
• Left mouse button drag-and-drop rotates the model;

• 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.

7.2.1. The volume modelling buttons from right to left:
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
Reset the model position to the starting position
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.

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 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 movement forces navigation up and down the
dataset in the Z axis)
Toggle XYZ 3D direction key
View the model in volume rendered model mode
View the model as an attenuation map
View the model as a maximum intensity projection
View the current cross-section of the dataset as a “volume plot” where local grayscale is
indicated by colour-coded height of the spikes (see below):
Volume rendered model Attenuation image (fwd.-proj.)

MIP image Volume plot of a cross-section
A clip box can be applied to a displayed model. Left button drag and drop while holding down
the keyboard shift button 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.
Similarly a clip plane can be used in a similar way as the clip box (left).
A navigation clip plane also shows an intersection with the volume model (red colour), but this
allows navigation in the Z direction in the dataset, since movement of the navigation clip plane

controls scrolling up and down the cross-section levels in the CTAn dataset and cross-section image
panes (right).
Note that translational movement in the CTAn volume model window is done by holding the
keyboard CTRL button at the same time as left mouse button drag and drop.
The yellow square in the bottom right corner of the volume image window shows translational
movement by showing a second, displaced square (see images above).

8. First Page: 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 further four buttons
representing various functions. These will be described in this chapter on the raw images page.
8.1. The profile bar (with MIP and other imaging

functions)
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 activate the profile bar, click on the profile line button at the top button bar (circled in red):
When this bar becomes active, a red line appears on the cross-section image. This line can be re-
drawn anywhere on the cross-section image by left mouse drag-and-drop, with its beginning marked
by a small circle. In a bar to the right of the cross-section 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).
On the panel above the profile graph there are six buttons which give access to the following
commands:
1. 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
2. Cut single slice – creation of a single longitudinal section cut along the profile line
through the dataset, within the limits of the region of interest.

3. Cut multiple slices – creation of a new set of images consisting of longitudinal
section cuts along lines parallel to the profile line.
4. Maximum or minimum intensity projection (MIP) – MIP images can be taken

orthogonal to the profile line or axially in the z axis.
5. A virtual projection image – a projection image is recreated by forward projection

from the cross-sectional dataset, from a selected perspective
6. Apply or remove the ROI – alternate between display of the image inside the ROI
only and display of the full image
8.1.1. Save profile

When the save profile button is pressed, the profile of density along the profile line, as displayed in
the profile window, is saved as a text file:
The start point of the profile line is indicated by the red and white bead at one end.
8.1.2. Single section reslicing

Clicking on the single scissors icon generates a single longitudinal cut along the red profile line:

In the image dialog the first button saves the single displayed image only, the second button
applies the displayed resliced image as the dataset _spr image to generate the projection
image, and the third button exits the dialog.
8.1.3. Multiple cross-section reslicing

Clicking on the multiple-slice scissors icon allows a multi-layered longitudinal cut along the
selected profile line, so that a deep section of the dataset – up to the whole dataset – can be
longitudinally resliced.
The parameters for constructing such a longitudinal section dataset are set in the dialog box which
appears. 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.

Simultaneously with modifying these parameters, the area selected for longitudinal resampling changes in
real time in the cross-section image window. The areas outside of this selection are inverted. While multi-
reslice is active, the cross-section image background is displayed as pink.
On pressing the OK 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 cross-section image corresponds to the current
position selected by the slider.

In the resliced images dialog box there are two save buttons, the first to save the single displayed
image only, the second to save the whole stack of resliced sections. The next button allows the
currently displayed image to be saved as the spr image to provide the projection window image, while the
last button exits the dialog.
8.1.4. 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.

8.1.4.1. MIP options
• 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.
• 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 densest 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.
• Depth of projection:
This sets the number of image slices in the chosen plane that will be sampled, centered
around the current cross-section 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.
• 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 cross-section 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 images created by the MIP
tool in the x (horizontal), y (vertical) and z (between cross-sections) planes, from the scan of a
Microfil-infiltrated kidney, are shown below.
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.

(1) Kidney microCT scan: (2) Kidney microCT scan:
cross-section xxxxxxxxxxxxxxxxxxxxxxxMIP, X plane (along profile, horizontal)
(2) Kidney microCT scan: (4) Kidney microCT scan:

MIP, Y plane (along profile, vertical) MIP, Z plane (“horizontal”)
8.1.4.2. The virtual projection image

The button for projection creates a virtual projection image by forward-projection from the
cross-section dataset. Like the MIP function, you can choose the “projection view” between
“horizontal” (i.e. operating in the axial Z plane to create a horizontal projection) and along profile,
where the direction will be orthogonal to the projection line.
The same options of background colour, depth and number of projections apply to the virtual
projection as to the MIP, as described above.

The generated image can, again, be saved or set as the dataset spr projection image.
8.1.4.3. Apply or remove the ROI
The last button to the right under “profile” applies or removes the current ROI from the displayed
image in the raw images page.
Note that when the ROI button is pressed and the Roi is applied, then this will apply to all the
sectioning and MIP / projection imaging functions associated with the profile line. Thus MIP images,
cut slice images and virtual projection images generated at this page will be restricted to the ROI if
the ROI button is selected.
If this button is not selected, then the MIP images, cut slice images and virtual projection images will
be made from the whole images, regardless of any ROI selection at the ROI page.

At the ROI page the ROI as shown (rotated rectangle) is applied
Back at the raw images page, the ROI button (far right) is selected, so the ROI from the ROI page is
applied to the displayed cross-section image in the raw images page.
At the raw image page if the ROI button (far right) is deselected, the ROI from the ROI page is not
applied to the image – the whole image is shown.
8.1.5. The ruler and protractor tool

Free-hand drawing a line with left mouse button on the cross-section image will activate a ruler tool
which measures straight line distance, as shown in the image below:

If the drag-and-drop is accompanied by pressing CTRL on the keyboard, then a protractor tool is
activated, as 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 ruler and protractor are only displayed while
the left mouse button is pressed.

8.2. 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
cross-section images. The tool dialog is opened with the yellow protractor icon in the CTAn top
button row:
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.
8.2.1. 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.
8.2.2. 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.

8.2.3. 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.
8.2.4. Coordinate measurement with the manual “measure” tool:
With this fourth tab selected, left mouse clicks record the XYZ coordinates of the clicked point.

8.2.5. Measure tool function buttons
Autofill On completion of each mouse operation, the measurement of the marked item will
be automatically added to the displayed data list.
Clear The displayed list of measurements will be cleared.
Save By clicking on the save button, all currently displayed measurements 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”.
Close Closes the measure tool.

9. Second Page: Region of interest
Moving to the second, region of interest (ROI) step or page, allows you to delineate regions of
interest on dataset images.
At this page, the image has a red highlighting (or blue if the image is inverted) – the highlighted
region is the selected region, or “region of interest” (ROI) for that cross-section. By default, the whole
cross-section is included in the ROI.
9.1. A note on terminology
The region of interest (ROI) refers to the selected region, either fixed shape of free-hand drawn, on a
single cross-section image.
The 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.
9.1.1. This is the row of function buttons at the ROI page:
Their functions are described below:
Load ROI Loads an ROI from a .roi file or from a stack of 1-bit binary images
Load external An external image, if in the 1-bit binary format, can be loaded to the current
image as ROI cross-section as the ROI for that cross-section
Save ROI Saves to file the sizes, types and positions of all 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).
Save ROI dataset Save a new dataset with images cropped to within the ROI only, restricted to
the range of slices set in the ROI.
Cut edited ROI Cut the edited ROI level (for pasting elsewhere)
level
Copy edited ROI Copy the edited ROI level (for pasting elsewhere)
level
Paste edited ROI Paste the (cut or copied) edited ROI level
level
Switch to nodes Toggles the edited ROI boundary between displaying connected nodes (“join
outline the dots”) and a smooth outline with corner nodes only

ROI shape drop- Opens the drop-menu for ROI shapes
menu
ROI added shape Choose the shape of added ROI objects made by right button plus shift (add
menu shape) or control (subtract shape)
Expand ROI Stretches the active fixed region of interest up to the size of the cross-section
image
Copy edited ROI to Copies the edited ROI shape to all images of the open dataset
all levels
Reset / delete ROI Deletes all edited ROI shapes, resets the default (ROI = whole image)
Invert edited ROI Inverts the edited ROI shape. What was outside the ROI becomes inside, and
vice versa.
Toggle ROI Alternates between three interpolation algorithms for edited ROI shapes: static,
interpolation dynamic and adaptive (adaptive is a mix of static and dynamic).
algorithm
If you select the ROI shape drop menu there is a choice of seven ROI types:
Rectangle
(Can be rotated if reset to “image” )
Square
(Can be rotated if reset to “image” )
Ellipse An ellipse
Round A circle
Polygonal A multi-nodal editable polygon
Empty / deleted Indicates no ROI is selected for this level
Interpolated Sets the current ROI as the interpolation of the closest neighbouring edited
ROIs above and below
Image format Sets the ROI to image format, allowing additional editing options such as
rotation of the image. An externally loaded image set to ROI will take this
format
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.
The default ROI is the rectangular region which has the same size as a dataset image. For
square images it is possible to set as default a round region of interest (entered in quadrate
with same sizes as the cross-section image). Open the dialog File / Preferences and the tab
Region of Interest set the radio button to Round or Square.

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. Double clicking on the
displayed ROI size in the status bar will
open a window allowing you to adjust
the ROI’s size and position:
“Left” and “bottom” allow XY
movement of the ROI. “Width” and
“height” adjust the ROI size.
Note the “center align” option. With this checked, changes to ROI size will keep the center at the
same location, expanding or contracting the ROI symmetrically around the center.
Refer to this ROI size if you wish to apply repeatedly VOI volumes of identical size and shape.
Elliptic ROI Polygonal (freehand drawn) ROI
The whole ROI on a cross-section image can also be shifted by drag-and-drop with the left mouse
button. In the Status bar at the right the relative displacement (“ROI offset”) of the ROI shape will be
displayed.

If you start drawing a freehand shape with the left mouse button held down in the field of a cross-
section 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.
If 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.
9.1.1.1. ROI-related keyboard shortcuts:
Region of interest / Edited above: switches to the next edited region of interest Ctrl. +
located above the current image;
Region of interest / Edited below: switches to the next fixed region of interest Ctrl. +
located above the current image;
Region of interest / Last Modified: switches to the image containing region of Backspace
interest last subject to modifications;
9.1.1.2. Additional ROI functions in the Region of Interest menu:
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, while all other levels are shown as elliptic ROIs.
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 (.roi).

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).
9.2. 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 ROIs
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.
9.2.1. Note on custom processing:
When analysing datasets in custom 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.

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.

9.2.2. The dialog box for saving an ROI dataset includes these items
Name Enter the filename for the ROI dataset

File type Choose between BMP, JPG, TIF, PNG and RAW
Location You can (optionally) choose a subfolder to contain the new images of the ROI
dataset. It is strongly recommended that you always save an ROI dataset in a subfolder. Note that
when you click on “browse” the file save window will always default to the location of the current
dataset, so that if you then click on “make new folder” its location will be by default as a subfolder of
the current dataset.
Create folder If this is selected then a the ROI dataset images will be
named “VOI” automatically saved into a subfolder named “VOI”.
Save ROI-file A copy of the ROI file (.roi) will be saved in the ROI dataset, re-formatted to the
smaller size of the ROI dataset (note: this is not a copy of the original .roi file). Save-ROI should
always be ticked unless you wish to rotate the ROI dataset.
Save overlay With this selected, a mask shape of the ROI is added to every images
saved cross-section, with greyscale
Rotate dataset In the case that “Save-ROI” is deselected, then the option will appear to rotate the
ROI dataset counter-clockwise by a specified angle in degrees
. The option “interpolate” will interpolate pixel grayscales in

rotated saved images to remove artefacts of pixel-shear.
Background The background (out of ROI) colour in the saved ROI images defaults to the original
dataset background colour, but can be set to black or white. (Normally leave it as it is.)
Restart with new If this option is checked, then as soon as the ROI dataset is
dataset saved CTAn will automatically open this dataset, and go to the
ROI page with the ROI loaded (from the re-sized .roi file)).
Note: The “Save overlay images” option changes the greyscale image. It creates a visual mask
indicating the ROI area by slightly increasing the greyscale of all pixels within the ROI. (So better not
to use this option if you need to measure density within the VOI.)

Left: Drawn ROIs, and Right: The saved ROI dataset images when “save overlay image” is selected
9.3. 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 fixed distance
away 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 cross-
section image (bottom left) – this is level 231. (Note that how a reference level is repeatably selected
may depend on a user’s 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.)

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 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 negative 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.
From the above image also, please note 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 <CTRL+Home> and <CTRL+End>
respectively.
9.4. Drawing multiple ROI shapes, and cutting

subtractive regions
Right mouse button click actions at the ROI page allow the creation of multiple ROI shapes, and also
of editing an existing ROI shape by subtraction.

9.4.1. Adding additional ROI shapes
Right mouse button drag-and-drop with the SHIFT button held down will allow additional ROI shapes
to be drawn.
By default, the additional drawn objects are freehand polygonal ROI shapes.
However by making a selection in the second shape drop menu in the ROI page button bar, just to
the left of the main drop menu of ROI shapes, it is possible for additional shaped drawn with right
button drag-and-drop plus SHIFT, to be either rectangular or elliptical:

9.4.2. Removing or subtracting from an ROI shape
Right mouse button drag-and-drop with the CONTROL button held down will make a subtractive
shape, that will cut the drawn shape out of existing ROI objects over which it encroaches. Again, by
default, the subtractive region is a polygonal freehand drawn shape. However by the second, right
hand drop menu of additional shapes, the subtractive drawn shape can also be a rectangle or an
ellipse.

10. Third Page: Binary selection
Moving on to the third, Binary selection 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.
10.1. 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.
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 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.
In the histogram window and table the current binary selection

is highlighted by white colour, with non-selected parts shown
highlighted in light brown. To change the boundaries of this
selection use the two sliders located above and below the
histogram window. To the left of this window is a vertical slider
for histogram scaling.
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 mouse button anywhere
in the histogram window.

10.1.1. Commands of the Histogram menu:
Histogram / Save Histogram : saves in a text file (prefix_hist.txt) the values of the histogram
table displayed at the given moment;
Histogram / Save Auto threshold : automatically assigns a threshold selection using the
Otsu threshold method (Otsu 1979, also see http://en.wikipedia.org/wiki/Otsu's_method )
Histogram / Logarithm scale : switches the histogram display mode between linear and
logarithmic;
Calibration : Implements density

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), on re-opening the
window.
Note – the “HUcal” calibration
number shown at the bottom of the
window is the calibration factor that
can be imported into NRecon, in order that reconstructed datasets can have HU calibration
embedded into them. It can be written to the scan log file prior to reconstruction in
NRecon. It can also be written into the control software of in vivo scanners such as the
SkyScan 1276 and 1278.
Histogram / From Image : shows the histogram distribution of brightness from the whole
area of the current image only.
Histogram / From Dataset : shows the histogram distribution of brightness 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-3 calcium hydroxy-apatite.
Attenuation coefficient : Sets the displayed density scale to units of attenuation coefficient
(−  .t )
(µ) according to I1 = I 0e

Histogram / Halftone view – displays the original grey level image with green highlighting,
with the binarised part of the image superimposed in red;
Histogram / ROI view – displays the part of the image inside the ROI in black and white,
and the region outside the ROI under green shading;
10.2. BMD calibration by the histogram tab in

preferences
The histogram tab in preferences allows bone mineral density (BMD), defined as g/cm3 of calcium
hydroxyapatite, to be calibrated against the density scales of either Hounsfield units (HU) or
attenuation coefficient.
The button “calibrate” allows a choice of calibration of BMD against Hounsfield units or attenuation
coefficient.

In the case that Hounsfield units are selected, a “default” button appears which sets a default BMD
relationship, a published value from clinical CT:
This value can be a default for use of CTAn in clinical CT analysis but will not be appropriate for
microCT 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 Bruker-microCT have BMD values of
0.25 and 0.75 g.cm-3.
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.

10.3. 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.
The four image modes shown below are selectable by switching the options for halftone-binary
image view and ROI-full image view.
10.4. File menu items at the histogram page
File / Save Binary – saves the dataset as binary images with the current 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.
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; (ii) 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 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, µm, 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.
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 the Polygon File Format or the Stanford Triangle Format (
http://en.wikipedia.org/wiki/PLY_(file_format) )
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.

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
Bruker-microCT 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 algorithm.
If you choose Adaptive Rendering, configuration boxes will appear in which you should
specify the “locality” and “tolerance” variable parameters.
10.4.1. The Locality and tolerance parameters for adaptive rendered 3D

models
• Locality: this parameter defines the distance in pixels to the neighbouring 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.
• 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.
It is possible to display or hide the Histogram bar from the menu View / Histogram.

11. Fourth Page: Morphometry
The morphometry calculation page (the 4th 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
(3rd) 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 moving to the morphometry page, a menu and
bar with the title Analysis will appear to the right of the cross-section image window, in which you
have access to morphometric analysis commands.
11.1. The 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 cross-
section 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.
11.1.1. Commands of the Analysis menu:
The commands shown to the right are listed by right

click in the analysis histogram pane:

Measures and outputs the 2d morphometric parameters of all
discreet binary objects on the current cross-section image.
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.
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.
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.
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 filename “datasetname_dst.txt (or .csv), short for
“distribution”. When this save distribution operation is selected, a window opens as shown below:
Note that there are tick-boxes 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 colour-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 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.

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.
This button displays the numerical value associated with each

histogram bar.
In the
case that length (diameter of area-equivalent circle) is
chosen as the histogram option, this button opens a
dialog box allowing you to specify the intervals of the
histogram of length values. This customised set of
intervals can be saved.
Sets the unit on the y axis of the displayed histogram, to object size
(diameter of area-equivalent circle).
Sets the unit on the y axis of the displayed histogram, to object length
(maximum distance between two object pixels).
Sets the unit on the y axis of the displayed histogram, to object

perimeter.
Sets the unit on the y axis of the displayed histogram, to form factor.
Sets the unit on the y axis of the displayed histogram, to

orientation.
Sets the unit on the y axis of the displayed histogram, to porosity

(percent area of fully enclosed space in 2d).
These above functions correspond to the rows of buttons and tabs above the histogram, in the
analysis window, shown below:

11.2. 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 cross-section 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 with a single line of data corresponding to the selected binarised object.
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 Shift 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 Ctrl held down. However the cross indicator will only light up
for singly chosen objects.

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.

You can save the results of individual analysis of image objects as a text file by 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 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.
11.3. 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 object analysis, on clicking the button to start
individual 3d analysis, no window will open to prompt for output filenames, etc. – instead the
calculation will begin immediately. File saving will be possible after analysis is complete.

When the calculation is complete, the following results window will appear:
In the 3D as in the 2D individual object analysis, if you highlight a row (above), the corresponding 3D
binarised object will be indicated by a target symbol at the centroid position of that object (see
below for example). Note that the centroid is defined in 3D, so in the case (that will frequently occur)
that the object is highly interconnected and extends over a significant volume, the centroid can be in
empty space.
Note also 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.
11.4. Analysis of all objects in 3d
Analysis / 3D analysis – initiates three-dimensional (3d) image analysis of binary selected

objects (white colour) within the volume of 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 Continue 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.

The list of 3D morphometric parameters available for analysis, shown after clicking on the “3d
analysis” button.
The window displaying results after running the “3d analysis” function. The “i” button 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.

11.4.1. Single line text output for automatic creation of table of results
from multiple datasets
If single text line is selected, results of each analysis are saved as one text line (comma delineated).
The file can be appended to with 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 spreadsheet 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:
11.4.2. Mean intercept length analysis (pane in Advanced preferences

tab)
For parameters based on Mean Intercept Length (MIL) such as Degree of Anisotropy you can select
the distance between secants (test lines). 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.

Adaptive spacing sets test line spacing to a distance rather than number of pixels. Fixed spacing sets
test line spacing to a number of pixels independent of pixel size.
Selecting the option “Perform advanced 3D stereology” enables the output of the full stereology
analysis results. These include the principal orientations and all MIL statistics, the tensor eigenvectors
and also some morphometric parameters calculated from the MIL analysis. Without this option
ticked, the 3D results will include only the degree of anisotropy and the three tensor eigenvalues.
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.
If 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.csv”. In this case the “i” 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).
You can save the results of 3d analysis as a table text file, by pressing the 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.
11.4.3. Advanced options for 3D morphometric calculations
In the advanced tab of the preferences, there are four tick-box items at the bottom: these are:
• Use all processors. This is an option that addresses limitation of processors available to CTAn
when other resource-hungry programs are running (such as NRecon). It helps CTAn to
increase the number of processor threads that it gets.
• 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. In CTAn version 1.18.8.0 this option is moved
into the box with MIL analysis, here in the same “Advanced” preferences tab.
• 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.
• Show the results based on direct counting of pixels / voxels. This applies to 2D analysis only
– it activates the output of alternative values of some parameters such as object volume and
surface area, marked with an asterisk “*”, where sub-pixel interpolation – such as by the

Pratt algorithm – is excluded, and values are based on counting areas and perimeters of
whole pixels only.
• Cache images (requires the dataset reload); this option is discussed in section 4 under
opening of datasets.
• 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.

11.5. 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.
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.
It is possible to display or to hide the Analysis bar with the menu View / Analysis.

12. Fifth Page: 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 5th, custom processing page using the button , 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.
 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 ... .

In the opened dialog, 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 CTAn 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.

12.1. The Plug-Ins bar
12.1.1. The Plug-Ins bar has the following five tabs
Collections – A set of most-used task lists can be kept in the Collections tab: a kind of cache for quick
access to task lists.
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 – Displays the full list of plugins available internally within CTAn
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 .CTAn.txt or .CTAn.log. Both output text files have
the same set of options. The button Open opens this file for viewing.
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 viewing after the execution of a single plug-in or list of plug-ins.

In the Plug-Ins bar there are commands which become active in some tabs and are disabled in
others:
12.1.2. The button bar in the Custom Processing page
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.
Pause – this button sets the task list to pause before running the selected plugin. This is
useful for testing and debugging of task lists.
Resume after pause – this button appears after a plugin has been set to pause. The button
will resume a paused task-list starting with the paused plugin. A plugin can optionally be
paused and re-started several times between start and finish.
Disable plugin – this button makes a plugin inactive so it will not run during the task list
operation. It will however remain in the task list and can be enabled by a second click.
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, 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 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 (.ctt file) the list of plug-ins shown on the Task list tab.
Plug-in configuration – shows the configuration dialog of the selected plug-in.
When you add any plug-in to a list on the Task list tab, it is copied with its current 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.
Batch manager – starts a new instance of the CTAn program in batch 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 view – viewing mode in custom processing, to view the whole original image, (i) in
the example below.
Image inside ROI view – viewing mode in custom processing, to view only the part of the
image inside the current ROI, (ii) in the example below.
ROI view – viewing mode in custom processing, to view only the current ROI itself as a
binarised image, (iii) in the example below.
Clipboard view – viewing mode in custom processing to view the clipboard, which is a third
image channel required for complex task lists. The contents of the other three image
channels (image, image-inside-ROI, ROI) can be copied to or from the clipboard at any time.

(i) Image (ii) Image inside ROI (iii) ROI (iv) clipboard
A keyboard shortcut allows you to jump between the four image channels (image, image-inside-ROI,
ROI, clipboard). This shortcut is the control button plus the numbers 1-4; so that
Ctrl + 1: shortcut to IMAGE
Ctrl + 2: shortcut to IMAGE-inside-ROI
Ctrl + 3: shortcut to ROI
Ctrl + 4: shortcut to CLIPBOARD
12.2. “BatMan” – the batch manager for automation
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 similarly to the elements in the Plug-Ins bar
in the custom processing page. Above the upper window are four tabs:
Collections – can keep a “cache” of frequently used task lists for quick access
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.
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:
Add adds the selected plug-in from the Internal or External tab to the list of plug-ins in
the Task list tab.
Remove deletes a highlighted plug-in from the list on the Task list tab.
Move up 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.
Move down 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.
Import reads from the disk a list of plug-ins (.ctt file) and shows them on the Task list tab.
Export saves to disk the list of plug-ins shown on the Task list tab, plus the configuration of
each plug-in, as a .ctt file.

In the lower dialog window there is the list of datasets to be processed, and to the right of this
window some buttons for customizing the list and controlling the batch processing:
Add adds a dataset to the list. In the opened dialog any image from a dataset can be
selected. A drop menu on the Add button gives options to load an ROI file, to load all
datasets within a folder, and to load a second dataset to the clipboard.
Remove removes the highlighted dataset from the list. A drop menu gives options to remove
several selected or all datasets
Properties Displays properties of a listed dataset such as path and pixel size; also gives options
for quick selection an de-selection
Results 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.
Report 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.
Import Imports a previously saved dataset list, in the “ctl” format.
Export Exports 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:

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.
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.
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.
The close button closes the BATMAN window, and stops batch processing if it is in progress.
When a batch task list is in progress, a progress bar will appear at the bottom of the window.
12.2.1. 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 status of the plug-in shown in real time during batch operation.

12.2.2. 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 .roi 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.
12.2.3. Preferences in BatMan
Right clicking on the top left corner of BatMan opens a preferences window.
The BatMan preferences are a limited set of the preferences in the main part of CTAn. One additional
preference is under the tab “tools”:

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 as set in the previous BatMan session.
13. 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.

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 Сustom text and Custom logo. When you select Сustom text from
the Layout Item list, the button Edit will appear. Pressing this button will open the Сustom 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. where CTAn.exe is located). If
this logo.bmp file is absent, a default Bruker-microCT logo is provided.
The drop menu Alignment in the group Snap 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.
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 Setup… button in the Print Layout dialog,
you can specify page size and orientation, select the
active printer and change its properties.
The Layout Item drop list can contain the following items:
Histogram of distribution – the image of the histogram of
distribution shown in the Analysis bar (2d parameters from
current image).
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.
Cross-section 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 “logo.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
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 Print 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 OK closes the Print Layout dialog and saves all modifications, whereas
the button Cancel closes the dialog without saving any changes.

14. References
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.
Feldkamp LA, Davis LC, Kress JW (1984) Practical cone-beam algorithm. J. Opt. Soc. Am. 1 (6): 612-
619.
Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3d surface construction algorithm.
Computer graphics 21 (4): 163-169.
Nobuyuki Otsu (1979) A threshold selection method from grey-level histograms. IEEE Trans. Sys.,
Man., Cyber. 9 (1): 62–66.
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.
Ridler TW, Calvard S (1978) Picture thresholding using an iterative selection method. IEEE
transactions on Systems, Man and Cybernetics 8(8): 630-632.
Straumit I, Lomov SV, Verpoest I, Wevers M. Determination of local fibers orientation in composite
material from micro-CT data. In: Proceedings of the 11th International Conference on Textile
Composites (TexComp-11) 2013 Sep 19.
Straumit I, Lomov SV, Wevers M. Quantification of the internal structure and automatic generation of
voxel models of textile composites from X-ray computed tomography data. Composites Part A:
Applied Science and Manufacturing. 2015 Feb 1;69:150-8.

15. Appendix A: Description of plug-ins in
custom processing
A description is provided here of the internal plug-ins in the custom processing and batch manager
modules of Bruker-microCT CT-Analyser.
Custom processing and memory management
When you move into the custom processing page of CTAn, a progress bar appears indicating the
creation of an additional copy of the currently loaded dataset within the computer’s memory:
This means that prior to working in custom processing, it is recommended to reduce the dataset to
the smallest size needed, since two and possible three copies of the dataset will be used by the
computer within custom processing (the third copy in case the “Clipboard” is used).
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 – rather than load full reconstructed datasets, if possible.
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 in a 64 bit
system it is advisable to have at least 32 GB of RAM in the computer in order for CTAn to have a good
working amount of RAM. In general, the more RAM the better – any quoted number will go out of
date within a few years.
For example, once you have selected your volume of interest (VOI) in the scan dataset at the Roi
page of CTAn, you should 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”.
The four image channels of custom processing

In the custom processing page there are four image views or channels: image, image-inside-ROI, ROI
and Clipboard. You can alternate between these four views either by clicking on the corresponding
buttons, or by the following keyboard shortcuts:
Ctrl + 1: shortcut to IMAGE
Ctrl + 2: shortcut to IMAGE-inside-ROI
Ctrl + 3: shortcut to ROI
Ctrl + 4: shortcut to CLIPBOARD

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 user’s own
software coded analysis function – communication with Bruker-microCT 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”.
The Preview Option

The plugins which modify the image in
either 2D or 3D, have a “preview” button
option which allows you to preview the
effect of the plugin in its current
configuration, on the currently selected
cross-section slice only. This option appears
at the bottom left of the plugin window
only when 2D space is selected.
Once a preview is run (but not before) a
rewind button appears just to the right of
the preview button. You can scroll to higher
and lower slices with Ctrl + ↑ or Ctrl + ↓.

15.1. Thresholding
This plug-in is where you set the two lower and upper thresholds for binarisation.
At the top of the plugin is the drop-menu to choose the type of thresholding. The thresholding
methods are listed below.
Please note that from version 1.19.10.2, there is an “Output to” field near the top of the Threshold
plugin. This allows you to output the thresholded image either to image, or to the region of interest
channel. If the latter, ROI, is chosen, this provides a quick way to perform “threshold masking”, that
is, to set the binary threshold of an image as a region of interest for analysis of either morphometry
or density.
Global: A fixed range of grayscales is set for solid pixels (white); pixels
outside this range are set as space pixels (black)
Adaptive (Median C): Adaptive thresholding: for each voxel, the threshold is calculated as
the median of all pixel/voxel grayscales within a selected radius.
Adaptive (Mean C): Adaptive thresholding: for each voxel, the threshold is calculated as
the mean of all pixel/voxel grayscales within a selected radius.
Adaptive (Mid-range C): Adaptive thresholding: for each voxel, the threshold is calculated as
the midpoint between minimum and maximum greyscales within the
selected radius.
Automatic (Otsu method): A single global threshold is set automatically using the Otsu method
(Otsu 1979).
Multilevel (Otsu method): A set of several global thresholds is set corresponding to two or
more density phases, automatically using the Otsu multi-level
method (Otsu 1979).
Two-dimensional Otsu: This is an Otsu method that is not a global but a local threshold,
adapting to surfaces as well as grey scale distribution. Note – here
Automatic (Ridler-Calvard): This is an automatic threshold algorithm similar to Otsu automatic
global threshold finding.

Automatic (Quantile): This method automatically sets a global threshold according to a
quantile fraction that corresponds to the integrated number of
voxels with greyscales up to and including the threshold.
Automatic (Mean): This method automatically sets a global threshold that is the mean of
the greyscale of all the image voxels
Automatic (Mid-range): This method automatically sets a global threshold that is half way
between low and high density class values. It tends to find a
threshold that is on the high side.
Automatic (Triangle): This method
automatically sets a
global threshold that
is the apex of a right-
angle triangle where
the other two points
are the low density
peak and the
histogram maximum
(see image right). It
tends to find a
threshold that is on
the low side.
Hysteresis: This method involves “seeds” of higher density. A low and a high
density threshold are set. Objects segmented with the low threshold
are only retained if they contain or are in contact with a seed
segmented by the high threshold. This can help remove low density
noise objects (with no seed).
High density
Low density
Thresholded (seed present) Not thresholded (no seed)
15.1.1. Adaptive thresholding

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.
The radius defines the circle within which the threshold is calculated, using one of the three methods
(median, mean, mid-range). The constant applies an offset to the minimum density contrast
recognised by the thresholding. Increasing constant can remove noise-associated structures.
Adaptive thresholding can be applied in 3D (analyses sphere around each voxel) or 2D (analyses circle
around each voxel). The 3D method is more accurate but takes significantly more processing time.
Note that a pre-threshold can be applied. The pre-threshold effectively delineates a marginal band of
density near object surfaces within which adaptive thresholding is applied. All pixels below the low

pre-threshold (here 40) are set as black (space). All pixels above the high pre-threshold (here 125)
are binarised to white. (Note – when a pre-threshold is applied, then you do not need to set a
constant, and the constant value can be left at zero.)
If all objects are thin, then the upper pre-threshold can be set at 255. However if there are thick
objects, an upper pre-threshold of 255 results in artificial holes in the middle of thick objects. To
prevent this, set a suitable upper pre-threshold <255.
(a) (b) (c)

(a) A low pre-threshold of 40, (b) a high pre-threshold of 125, (c) the resultant adaptive thresholded
image.
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
example to the “reload” plug-in.
15.1.2. Otsu and Ridler-Calvard thresholding

Otsu thresholding with a single level can be applied either in the binary page or by choosing the
“automatic (Otsu method)” option in the threshold plugin. Mathematically, the Otsu method
exhaustively searches for the threshold that minimizes the intra-class variance, defined statistically as
a weighted sum of variances of the two classes (Otsu 1979).
Please see: https://en.wikipedia.org/wiki/Otsu%27s_method
The Ridler-Calvard method is mathematically similar to the Otsu method (Ridler and Calvard 1978).

Multi-level Otsu thresholding allows three or more density phases to be segmented automatically,
not just black and white. The number of phases identified is one more than the number of thresholds
that you choose, so if you set 2 thresholds you get three density phases.
The following variables must be selected for multi-level Otsu thresholding:
• 3D/2D space: As with most plugins, Otsu thresholding including multi-level can be applied in
3D or 2D space.
• Number of threshold levels: choose the number of density phases to be assigned
• Inside VOI: select this to restrict the
Otsu calculations to voxels within the
VOI only. Note – this is an important
parameter, including or excluding
outside-VOI voxels with different grey
scale distribution to inside the VOI,
will influence the calculated threshold
values.
• Output colour of class thresholding:
this selection determines the grey
scales that are assigned to the density
phases calculated by multi-level Otsu.
The image output by multi-level Otsu
will have a number of grayscales equal
to the number of threshold levels
selected.
o If “mean intensity in class” is selected, then the grey scale for each phase is the mean
of the grayscale range of that phase;
o If “threshold level of class” is chosen, then the grayscale output for each phase is the
same as the lower threshold of that phase;
o If “class id” is chosen, then the grayscale output will take the grayscales 1, 2, 3 etc.
for each density phase. This option is useful where multi-level Otsu is applied in 2D,
since different thresholds are applied on every level, and it simplifies analysis is the
respective levels are given the same grayscale values on each output image cross-
section. However the resultant images in this case look very dark or black due to the
low grayscale values. In this case – as shown below in the description of the
arithmetic operations, using the multiply (“MUL”) operator in arithmetic operation
can increase the values for instance to 20, 40, 60 etc. moving them into the visible
range.
Please note – the images output by the multi-

level Otsu operation, while having very few (3
or more) grayscales, are not binary images
but grayscale images; thus they cannot for
example be saved in the monochrome, 1-bit
format.
The 2D Otsu method is automatic and locally
adaptive. There is a radius to set – as radius
increases, more small pores or features are
excluded and the resulting binary effectively
smoothed to remove the smallest details. 2D
Otsu does not mean it operates in two

dimensions only. It mean it uses two parameters – greyscale and nearness to a surface, as opposed
to the simple automatic Otsu which analyses the grey histogram only (“1 dimension”). 2D Otsu by
contrast is not a global threshold but a locally adaptive one. It is useful when segmenting porous
material in images that are noisy, such as of a dense matrix like rock or bone.
15.1.3. Other automatic statistical methods and hysteresis thresholding

Also in the list of threshold types are automatic methods of finding a global threshold that are based
on simpler mathematical methods than the Otsu or Ridler-Calvard methods. These are the quantile,
mean, mid-range and triangle methods, that are explained briefly above in the list of threshold
methods. Hysteresis thresholding which defines a high density “seed” threshold and a lower density
general threshold, is also described above.
15.2. 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 5th 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, jpg, png, tif and Raw data can
be selected.
15.2.1.1. There are five tick box options in “save bitmaps”:
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.
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 set 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.
Save only the current slice: Only the single current cross-section will be saved.

15.3. 2d analysis
This plug-in runs 2d line-by-line analysis of the ROI part of all dataset images.
You can select the output of the “summary results” only, the full line-by-line data (“individual
results”), or both summary and full data together (“all results”).
Note that to the

right of the
“individual results”
and “summary
results” options,
there is a
“customise” button.
Clicking on
“customise” opens a
window with a list of
all the summary and
individual 2D
parameters,
respectively, with
tick boxes to select
or deselect each
parameter.

15.4. 3d analysis
This plug-in runs 3d analysis of the ROI part of the loaded dataset.
The configuration dialog for this plug-in is the similar to that for 3d analysis at the 4th, 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 comma-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.
When thickness and / 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 Bruker-microCT
Dataviewer. Under the colour drop menu, choose colour 1 or 2. Then the bar under “Colour / data
range” will become coloured. At first the image will usually look very dark with little visible. You need
to move the upper colour slider and move it down from its default value of 100. In the example
below it is reduced to 14. Adjust the colour slider to obtain a good range of colours corresponding to
thickness.

15.5. Filtering
The filtering applies several smoothing and sharpening operations to the loaded images.
This 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.)
There are three things to choose in the configuration dialog for the filtering plugin:
• The filter type (Gaussian blur, Median, Uniform, Kuwahara, Unsharp mask, Conditional mean,
Contrast stretching, Contrast enhancement, Anisotropic diffusion)
• 2d or 3d smoothing (3d smoothing averages image pixel data vertically in the z axis as well as
x and y)
• The radius of smoothing (applied either in 2d or 3d) in pixels/voxels.

15.5.1. The Unsharp mask
The unsharp mask is a means of sharpening images (despite the confusing name suggesting the
reverse). The method works by (a) making a blurred version of the image, (b) finding the difference
between the original and the blurred images, and (c) adding this “difference” image to the original,
resulting in an enhancement of the edge details that are removed in the blurring.
The unsharp mask has the following adjustable parameters:

• 2D/3D space: the operation can be carried out in 2D or 3D
• Radius: the radius of operation of the unsharp mask
• Amount: this is listed as a percentage, and controls the magnitude of each overshoot (how
much darker and how much lighter the edge borders become). This can also be thought of as
how much contrast is added at the edges. It does not affect the width of the edge rims.
• Threshold: controls the minimum brightness change that will be sharpened or how far apart
adjacent tonal values have to be before the filter does anything.
Unsharp masking is described on wikipedia: http://en.wikipedia.org/wiki/Unsharp_masking

Here are the descriptions of “radius”, “amount” and “threshold” from this wikipedia article:
Radius affects the size of the edges to be enhanced or how wide the edge rims become, so a smaller
radius enhances smaller-scale detail. Higher Radius values can cause halos at the edges, a detectable
faint light rim around objects. Fine detail needs a smaller Radius. Radius and Amount interact;
reducing one allows more of the other.
Amount is listed as a percentage, and controls the magnitude of each overshoot (how much darker
and how much lighter the edge borders become). This can also be thought of as how much contrast
is added at the edges. It does not affect the width of the edge rims.
Threshold, the restriction of the function to larger intensity intervals, can be used to prevent smooth
areas from becoming speckled. The threshold setting can be used to sharpen more-pronounced
edges, while leaving subtler edges untouched. Low values should sharpen more because fewer areas
are excluded. Higher threshold values exclude areas of lower contrast.

(a) (b) (c)
Images of a mouse (B6) femur scan, SkyScan 1174, processed to improve detail resolution. (a)
Original reconstructed image; (b) after running unsharp mask, two times, with 2 pixel radius in 3D,
threshold 0; (c) the sharpened image slightly smoothed to de-noise with Gaussian blur, 3D, 0.5 pixel
radius (after each unsharp iteration).
15.5.2. Conditional mean

The conditional mean is an edge-preserving smoothing filter. It smooths between neighbouring
voxels only when the difference of greyscale between the two voxels meets a set condition.
The radius is the kernel radius of smoothing.

The threshold is a maximum difference in greyscale between two neighbouring voxels – expressed as
a percent – where smoothing will take place. Where neighbouring voxels differ in greyscale by more
than this percent, then smoothing is not applied. This is the basis of edge preservation. To increase
edge preservation, lower the threshold, and to reduce edge preservation increase the threshold. You
can start with a value in the range 10-30 and then find the best value.
15.5.3. Contrast stretching

Contrast stretching pulls the minimum greyscale in the histogram down to zero and the maximum
greyscale up to 255, the upper grey scale. If the minimum and maximum grey scales are already 0
and 255 then this plugin will not change the image.

15.5.4. Contrast enhancement
Contrast enhancement has a stronger effect than contrast stretching. The sigmoidal, asymptotic
curve representing cumulative voxel number with incrementally increasing greyscale is pulled into a
straight line, changing the greyscale distribution in a way a bit similar to a log transform.

15.5.5. Anisotropic diffusion filtering
Anisotropy diffusion filtering is edge-preserving smoothing. “Diffusion” implies no overall increase or
decrease in intensity, i.e. no creation or destruction of intensity signal: good for density
measurement. “Anisotropic” implies not oriented uniformly, instead smoothing follows local
orientation according to a fitted diffusion tensor. Anisotropic diffusion equations can’t be solved
analytically so require numerical solution – therefore the method is iterative – you need to specify
how many times it will run.
Privilege options are available to preserve either high contrast surfaces or wide regions. The gradient
threshold determines the sensitivity to surface gradient – a good starting value is 5. Iteration number

also should be selected – 10-20 is a good starting range.
Anisotropy diffusion filtering smooths tooth tissue while preserving edges and cracks.
15.6. 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).
Erosion: Removal from the surface of binarised objects the selected number of pixel layers
Dilation: Adding to the surface of binarised objects the selected number of pixel layers
Opening: Erosion followed by dilation, both actions with the selected number of pixels
Closing: Dilation followed by erosion, both actions with the selected number of pixels
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.
Under “type” choose between erode, dilate, open and close. Set the procedure to 2d or 3d. You can
set the morphological operation kernel to square or round (round is better). The radius of the kernel

is specified in the “radius” box. 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. After “apply
to” please specify image or ROI.
Here are some examples of the effects of erosion, dilation, opening and closing:
1. Erosion, 1 pixel (hint - blocks are three pixels wide)
2. Dilation, 1 pixel
3. Opening, 1 pixel
4. Opening, 2 pixels
5. Closing, 1 pixel
6. Closing, 2 pixels

15.7. 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.
In configuring the despeckle plug-in, you set the box which is labelled “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”.
Here is a brief description of the available variations of despeckle:
Remove black speckles removes objects that are black (i.e. thresholded to represent space or
background) below (or above) a specified number of voxels.
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.
Enclosure 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).
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.

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.
15.7.1. The RANGE despeckle option

In the despeckle plugin it is possible to select a range of object sizes – both white and black voxel
objects / pores. You can either delete objects / pores within a specified range, or delete all objects /
pores outside the range.

15.8. 3D model
This plug-in will build a 3D surface-rendered model of the current binarised objects inside the current
VOI (volume of interest).
Note that a model filename can be chosen by ticking “custom filename”.
15.8.1. Algorithm options for surface-rendered 3D models:
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 Bruker-microCT 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.
15.8.1.1. Type of file 3D model file formats:
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 Bruker-microCT 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 Bruker-microCT 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 not have the option for smoothing in CT-volume which is available for p3g models.
PLY A non-Bruker-microCT 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. 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,
µm, 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.
If you select the adaptive rendering 3d model algorithm, three further parameters need to be set:
Locality this parameter defines the distance in pixels to the neighbouring 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.
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.
Smoothing set on or off
15.9. 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.

Shrink-wrap works in the following way: Set an ROI around the outside of a study object – in the
given example a slice of mouse metaphyseal bone. This can be a loosely drawn ROI outside the
boundary, or just the default whole image ROI.
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 , you will see a
black binary mask indicating the current ROI.
Run the task 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 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 center 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.
15.9.1. The other shrink-wrap options:
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 cross-section images, and the fill-out function
will expand an ROI from the initial “seed”. This can be termed “seed-growing”.
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 object.
For most effective seed-growing by fill-out, choose the sub-option “trim the lumps” rather than
“remove pores”.

(a) A stained section; (b) a “seed” VOI; (c) fill-out fill-out with (d) “trim the lumps”
A 3D volume rendering of the results of seed-growing with fill-out in the Shrink-Wrap plugin.

15.10. Reload
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 – 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 cross-sectional 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.
15.11. Histogram
The density distribution of the loaded dataset can be output by the “histogram” custom processing
plug-in. Selection between 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.

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.
When 3d output is selected, the option to append summary results to a “line-by-line” text report file
becomes available.
The tick-box “Inside VOI” restricts the plugin output the histogram to the contents of the VOI.
15.12. 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 4th,
processed images page of CTAn, as described in chapter 11 sections 2 and 3.
15.12.1. Individual 2D object analysis

When you select 2D space for individual object analysis, the following window opens:

There are several options.
“Use Clipboard as density map” should be selected if you wish to include average “density” as one of
the parameters measured for each discreet object. For this to work, the Clipboard needs to be filled
with a copy of the image dataset before you run the individual 2D object analysis. This is done in
Bitwise operations with this COPY operation:
As we saw at the chapter on the density / binarisation page, there are four units of “density” of
which one should be selected in the ‘Density unit” drop menu. Note that if either HU or BMD are
selected, you need to ensure that the corresponding calibration has been done prior to the analysis.

“Save to Clipboard color-coded images”: A second way to use the Clipboard in 2D individual object
analysis, is to save to the Clipboard a copy of the dataset in which each discreet object is assigned a
greyscale corresponding to a measured parameter value of that object. To do this, tick the box “Save
to Clipboard color-coded images”.
The option “object label” gives each object a different color for the purpose of 3D visualisation, not
related to any object parameter. If this option is chosen, it is recommended to also select the linked
tick box on the right, “Random number”. This randomises the assignment of colours to the objects
and gives a better visual colour effect.
15.12.2. Individual 3D object analysis

In the case that 3d space (i.e. analyse individual objects in 3d) is selected, the following window
opens:
“Use Clipboard as density map”: The use of the Clipboard as a density map is available as in the
individual 2D object analysis (above). What is different in 3D is the way in which individual objects
are defined – by 3D connectivity of voxels (applying 6-adjacency).

“Save to clipboard color-coded images”: Likewise, in 3D analysis also the Clipboard can be populated
with a copy of the image dataset in which each discreet object (defined in 3D) is assigned a greyscale
corresponding to a selected measured 3D parameter of that object. This greyscale can be converted
to colour using a colour palette.
With “Save to Clipboard color-coded images” selected, there are additional options associated with
two of the available parameters. If “Orientation (Theta)” is selected, then by default the polar angle
theta is applied – an angle in 2D only – the equatorial or azimuthal angle (using ISO 31-11, and ISO
80000-2:20091). However a tick box to the right gives a second (and generally better) option, “sphere
section:
Sphere section outputs 3D angle as a limited number of 3D spherical segments defined by an angle. A
drop menu under the ‘Sphere section” tick box allows you to choose an angle between 90 and 15
degrees. A smaller angle such as 15 degrees gives better resolved spatial orientation information.
1 ISO 80000-2:2009. International Organization for Standardization.

At the bottom of the window there are further tick boxes. On the left are selections for three
additional parameters, SMI, major diameter and structure thickness. On the right is a tick box option
for saving the results – which can be quite voluminous – to a separate text file; this option is
recommended.
15.13. 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.
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 (image from ROI or ROI from image).
SWAP Swaps image and ROI (image becomes ROI, ROI becomes image).
NOR NOT and OR applied together (the inverse of OR)
NAND NOT and AND applied together (the inverse of AND)
Please note that the Bitwise operations can be applied to three variables, IMAGE, ROI and “value”.
Value means that a fixed number value can be set. Selection of “value” as one of the variables in a
Bitwise expression is not always appropriate. OR, AND, XOR and SUB are the operators which can
employ the “value” variable in the Bitwise plugins – applying it to the others, COPY, NOT and SWAP
will result in an error message.
15.14. Arithmetic operations
Arithmetic operations can be applied. These operations can be applied to three variables, IMAGE,
ROI and “value”. Value means that a fixed number value can be set. The operations are:

ADD the grey values of IMAGE and ROI are added for each pixel
SUB the grey value of each image pixel (IMAGE OR ROI) is subtracted from that of the
other image.
MUL the grey value of each image pixel (IMAGE OR ROI) is multiplied by either the grey
value of the corresponding pixel from the other image, or by a fixed value.
Note – an example of the use of the arithmetic function MUL (multiply) is for Otsu multi-level
thresholding, in the case where the output grey value is selected as “class id”. In this case the
multiple segmented phases are output as the grey values 1, 2, 3 etc., with very low intensity and not
readily visible. If you then multiply these grey values by a value such as 10 or 20, the density phases
become much more easily visible, as shown in the example below.
Top left: Cross-section of sand; Top right: Median filtration to reduce noise; Lower left: Otsu multi-
level (3) thresholding with “class id” chosen: segmented phases are given grey values of 1,2 and 3,
too low to be visible. Lower right: The arithmetic operation IMAGE = IMAGE MUL (value = 20) is run,
increasing the segmented grey values to 20, 40 and 60, making them easily visible.
DIV divide by
MIN find the minimum out of the two variables on either side of the operator
MAX find the maximum out of the two variables on either side of the operator

15.15. Geometric transformations
Geometric transformations allow translational movement and flipping of the images.
15.15.1. The five geometric transformations are:
• Flip vertical: the image or ROI is mirror-flipped vertically

• Flip horizontal: the image or ROI is mirror-flipped horizontally
• Translate: the image or ROI can be translated by a selected x/y shift
• Rotate by 180 degrees: the image or ROI can be rotated 180 degrees.
• Invert Z order: Inverts Z order – this can address 3D image format compatibility
If translate is chosen, enter the x and y shift – positive or negative – in the fields below.
15.16. Comment
Task-lists can be long and complex. Sometimes it is hard to remember the logic of a task list that you
have previously made – let alone one made by someone else.
The comment plugin offers the option to make task lists more transparent and comprehensible –
what is going on here? To annotate a task list, simply add a comment plugin at the start or end of a
set of operations. The text that can be types into the comment – up to 512 characters (4 times more
than you get on Twitter) can explain that part of the task list – for the benefit of you or someone
else.

15.17. Primitive ROI
The “Primitive ROI” is a single voxel deep VOI on one face of a dataset cube. Its purpose is for testing
connectivity across a volume, between opposite faces of a dataset cube. The Primitive ROI plugin
defines the six faces of the dataset cube as shown below, with respect to the cross-section image.
The primitive ROI consists of a single voxel layer on one of these faces, which is selected in the drop
menu:
The left and right and front and back edges are defined in the dataset cross-sectional plane, while the
top and bottom edge mean the first and last cross-section images in the Z depth direction. These
definitions are illustrated below:
Left / right edge

Front / back edge
Top / bottom edge
The second drop menu in the Primitive ROI dialog box offers three options for the type of ROI
created. If you select “Exclusive”, then the primitive ROI created will simply be a single voxel thick
layer occupying the whole of the selected face of the cube. This single layer selection of a whole face
is not influenced by the current image or ROI, when “exclusive” is selected.
However the other two options, “Infimum” and “Supremum” are options that set the ROI in relation
to the currently existing ROI.
Supremum: Least upper bound LUB “Maximum”

Infimum: Greatest lower bound GLB “Minimum”
Exclusive: GLB but extended to whole edge

15.18. Local orientation
The Local Orientation plugin provides a colour-coded map of local 3D spatial orientation of
structures. Note that local orientation is calculated from original greyscale images, not binarised
images, so you should not threshold prior to running Local Orientation. Local orientation is calculated
using the method of Straumit et al. (2013, 2015) to determine local anisotropy tensors in microCT
image data.
Like many custom processing plugins, Local Orientation operates in 2D or 3D space. If 2D is selected,
then you have a choice of radius in pixels. The angle output is the equatorial or azimuthal angle phi
(using ISO 31-11, and ISO 80000-2:20092).
If 3D space is selected then after “Output” there is a drop-menu choice of two units of angle, the
theta (the polar angle2) which is in one 2D plane only, or the “sphere section” which gives 3D
spherical angular segments defined by a selected angle. The smaller angle gives more sphere angular
segments and thus better resolution of orientation, so 15 degrees is the best option for angular
resolution.
2 ISO 80000-2:2009. International Organization for Standardization.

15.18.1. Binary masking of objects prior to running Local Orientation:
It is recommended to apply a “binary mask” ROI to a dataset before running Local Orientation. If you
run Local Orientation without any ROI applied, then the resulting images, greyscale coded for
orientation, are inflated beyond the borders of separate objects:
To avoid this problem, first binarise the fiber images, then copy that binary image to the ROI:
After the binary image has become the ROI, then reload the image. This process can be called the
“binary masking” of an object and is useful for a range of analysis or visualisation operations.

With a binary mask ROI applied in this way, the colour-coding can be applied to the volume of the
fiber elements only, not extending into surrounding space:
15.19. Compositing
A composite means a 2D projection from a 3D image volume using one of several techniques.
In this dataset of an ant, an individual cross-section does not contain much image data relative to the
whole animal. However a projection such as a shadow projection and visualise the whole ant:
Here a composite image will help us to see the whole ant by two projection methods: the maximum
intensity projection (MIP) and shadow projection. For both of these methods we can choose three
orthogonally separated orientations of the projection: Axial, coronal and sagittal:

The images that we obtain result from our choice of the compositing method, and the projection
direction. The tick-box “Show image” opens a window with the projected image once it is made:

16. Appendix B. Boolean image operations
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 Image inside ROI
function BITWISE BITWISE BITWISE BITWISE after BITWISE
operation operation operation operation operation
No BITWISE
operation
(default)
COPY
image =
COPY ROI
ROI = COPY
image
NOT (inverse)
image = NOT
ROI
ROI = NOT
image
image = NOT
image
ROI = NOT
ROI

OR (the sum)
image =
image OR
ROI
ROI = image
OR ROI
AND (the overlap)
image =
image AND
ROI
ROI = image
AND ROI
XOR (exclusive or; finds difference)
image =
image XOR
ROI
ROI = image
XOR ROI

BITWISE Image before ROI before Image after ROI after Image inside
function BITWISE BITWISE BITWISE BITWISE ROI after
operation operation operation operation BITWISE
operation
SUB (subtract)
image =
image SUB
ROI
image = ROI
SUB image
ROI = image
SUB ROI
ROI = ROI
SUB image
SWAP
Image =
SWAP ROI
ROI = SWAP
image

NOR (not or)
image =
image NOR
ROI
ROI = image
NOR ROI
NAND (not and)
image =
image NAND
ROI
ROI = image
NAND ROI

17. Appendix C: Format of the CTAn
command line
The command line of the CTAn program looks like the following:
CTAN [[/R|/T|/L]FILENAME] [/Nn] [/Dn] [/Ps] [/V] [/S] [/B] [/A] [/C] [/?]
where:
/R - load a ROI file
/T - load a task list
/L - load a list of datasets in the batch processing
FILENAME - full pathname of a dataset image or another file

when /R or /T or /L is specified (see below)
/N - the number <n> of digits in the postfix of filename

/D - decrease images <n> times
/P - set new <s> pixel size (mm)
/V - use averaging in 3D
/S - load single image
/B - start a program in the batch processing mode
/A - start automatically a task processing
/C - close a program when the batch processing is finished
/? - show this dialog box

Here is the full window of CTAn command line modifier syntax:
17.1. Examples of use: auto-analysis following NRecon

It is possible to set up CTAn to run a BatMan operation automatically following reconstruction of a
dataset in NRecon.
To do this, first turn on Engineering mode with Ctrl alt shift E.
Then go to Options, preferences, put CTAn to auto and press the three dots:

Next, go to the location of CTAn and select CTAn.exe (usually C:\\skyscanxxx\ctan.exe)
You will see this window:
Click “Yes”
You will be able to add a command line. The basic one will look like this:
/CAarg /n8 /b /o /c /a /t"C:\SkyScan1275\pfizer_tasklist.ctt”
/CAarg means: start CTAn with arguments (this should be in there)

/n8 means: number of digits is 8
/b means batch mode
/o – omit checking of data integrity
/c – close after task list is complete
/a is automatic mode
/t”CXXXXXXXXX” is the path to your task list.
/r”XXXXXX” is the path to your ROI

18. 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 surface 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
cross-sectional images where pixel values also indicate
brightness. In cross-section images high brightness equals
low x-ray density/opacity and vice versa.

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
temporary 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 cross-section 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 cross-section 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.
Cross-section image The “dataset” produced by Feldkamp cone-beam

reconstruction of the x-ray projection images, consists of a
stack of cross-sectional 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 saltatory reconstruction is selected (every two or more
slices). Cross-section images are produced by the Bruker-
microCT reconstruction program and can be written in 8-bit
bmp, 8-bit jpg or 16-bit tiff format.
CTAn The CT-Analyser program for dataset viewing, analysis and

3D model building.
CTVol The CT-volume program for viewing and manipulating 3D

models and making animated “movies”.
Dataset A stack of cross-section images made by cone-beam

reconstruction, constituting the 3d image of the scanned
object. Files can be in bmp, tiff or jpg format.

Dialog box A box opened onscreen by a mouse click or key stroke which
is interactive, allowing or requiring the user to enter
selections or information
Drag-and-drop 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.
Feldkamp 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.
Instance If 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 program
is called an instance.
Left-click Position the mouse cursor (arrow) over the screen object in
question, and press the left mouse button.
Live flag A tick box activating a function in real time in CTAn.
Micro-CT Computed tomographic imaging applied to small objects with

nominal resolutions (pixel sizes) in micron or submicron
range from 1-100 µm. Based on multiple x-ray transmission
images from incremental angular aspects over 180 or 360°.
NOT 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).

Otsu Otsu thresholding automatically segments one or more
density phases, using the Otsu algorithm which finds
thresholds that minimise inter-class variance of the grayscale
histogram (Otsu 1979).
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
microCT 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 particular option is
selected.
Reconstruction Reconstruction is the process by which, taking the set of

projection images as raw material, a dataset stack of cross-
section 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 (222). 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.
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 At the top of some windows and dialog boxes are tabs
resembling the tabs on the top of folders in a 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 cross-section 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 microCT 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.


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SkyScan CT-Analyser (“CTAn”)

CTAn User Manual 1.20 Jan / 2020 0

CTAn was created by Bruker microCT in Belgium

CTAn User Manual 1.20 Jan / 2020 1

3.2.1. Licensing of ANT with CTAn ............................................................... 11

3.2.2. Upgrades requiring license re-authentication ...................................... 11

4. Set-up of preferences ........................................................................................ 12

4.2. Brief description of the preference tabs ...................................................... 12

4.2.1. Preference tabs: introduction .............................................................. 12

4.2.2. Keyboard shortcuts in CT-Analyser..................................................... 15

5. Import and export of image files ........................................................................ 16

5.1.1. Conversion of different image formats at opening ............................... 21

5.2. Export of image files ................................................................................... 25

5.2.1. Export to AVI movie file ....................................................................... 25

6. The seven part structure of CT-Analyser: summary .......................................... 28

6.1.1. The volume rendering pane ................................................................ 31

6.1.2. The shadow projection pane ............................................................... 31

6.1.3. The dataset pane ................................................................................ 33

6.1.4. The cross-section image pane ............................................................ 35

6.1.5. The palette and analysis pane ............................................................ 38

CTAn User Manual 1.20 Jan / 2020 2

7.2. Launching volume modeling ....................................................................... 42

7.2.1. The volume modelling buttons from right to left:.................................. 43

8. First Page: Raw Images .................................................................................... 47

8.1.1. Save profile ......................................................................................... 48

8.1.2. Single section reslicing ........................................................................ 48

8.1.3. Multiple cross-section reslicing............................................................ 49

8.1.4. The maximum intensity projection (MIP) ............................................. 51

8.1.5. The ruler and protractor tool ................................................................ 55

8.2. The hand measurement tool ...................................................................... 57

8.2.1. Angle measurement with the manual “measure” tool: ......................... 57

8.2.2. Line measurement with the manual “measure” tool ............................ 57

8.2.3. Path measurement with the manual “measure” tool ............................ 58

8.2.4. Coordinate measurement with the manual “measure” tool: ................. 58

8.2.5. Measure tool function buttons ............................................................. 59

9. Second Page: Region of interest ....................................................................... 60

9.2. The “save new dataset from ROI” function ................................................. 64

9.2.1. Note on custom processing: ................................................................ 64

9.3. The reference level ROI tool ...................................................................... 67

9.4.1. Adding additional ROI shapes ............................................................. 69

CTAn User Manual 1.20 Jan / 2020 3

10. Third Page: Binary selection.............................................................................. 71

10.1.1. Commands of the Histogram menu: .................................................... 73

10.2. BMD calibration by the histogram tab in preferences ................................. 74

10.3. Modes of image view at the binary page: ................................................... 76

10.4. File menu items at the histogram page ...................................................... 76

10.4.1. The Locality and tolerance parameters for adaptive rendered 3D

11. Fourth Page: Morphometry................................................................................ 79

11.1.1. Commands of the Analysis menu:....................................................... 79

11.2. Individual object analysis in 2d: .................................................................. 82

11.3. Individual object analysis in 3d: .................................................................. 84

11.4. Analysis of all objects in 3d ........................................................................ 86

11.4.2. Mean intercept length analysis (pane in Advanced preferences tab) .. 89

11.4.3. Advanced options for 3D morphometric calculations .......................... 90

11.5. Analysis of all objects in 2d ........................................................................ 92

12. Fifth Page: Custom processing ......................................................................... 93

12.1.2. The button bar in the Custom Processing page .................................. 96

12.2. “BatMan” – the batch manager for automation ........................................... 98

CTAn User Manual 1.20 Jan / 2020 4

13. The printed report ............................................................................................ 102