Scanco User Instructions

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The micro-CT scanners in the lab are manufactured by Scanco Medical and most analyses are performed using their custom software. The micro-CT workstations run OpenVMS as its operating system and it is useful to learn some basic commands.

OpenVMS Basics

OpenVMS

OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.


Session Manager

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command $ vue .

Session

Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

Views (directory shortcuts)

The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

Commands and Utilities

Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

Applications

Under applications you can launch various applications including:

  • DECterm: opens a DEC terminal
  • MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
  • Mozilla/Netscape: opens a web browser
  • XV: opens a screen capture program


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DEC Terminal and Digital Command Language (DCL)

This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.

What is a symbol

DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols. Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL procedures, hold status information. 

$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]"	!A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS]	!Another way to define the symbol without quotations.
$ x == 3	                                !Store the value 3 in the symbol x.
$ SHOW SYMBOL x                                 !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x                        !Deletes the specified symbol, x.

Selected symbols on the Scanco system: 

$ UD	                            !Changes to the data directory.
$ UR	                            !Changes to the projects directory.
$ DISKS	                            !Shows the current disk usage.
$ DEC                               !Opens a new DEC terminal.
$ EVE file.txt                      !Opens the file in the text editor.
$ AIX file.aim                      !Shows the processing log for an aim file. 
$ AIX -L file.aim                   !The "-L" is used to show the full processing log.
$ QUE	                            !Shows all entries in the queue.
$ GS file.ps or file.pdf            !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq     !Shows scan information for an *.isq or *.rsq file.


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What is a logical

Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program. 

$ DEFINE UD DISK2:[XTREMECT2.DATA]   !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq  !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.

Selected logicals on the micro-CT system: 

COM            !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD             !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6            !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR             !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE             !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU             !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS    !Logical pointing to the results directory MICROCT_USER:[RESULTS]


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Arithmetic operations

Addition + The plus sign (+) adds two numbers.
Subtraction - The minus sign (-) subtracts the second specified number from the first specified number.
Multiplication * The asterisk (*) multiplies two numbers.
Division / The slash (/) divides the first specified number by the second specified number. If a number does not divide evenly, the remainder is lost. No rounding takes place.


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Logical expressions

And .AND. The operator .AND. combines two logical values as follows

true .AND. true = true
true .AND. false = false
false .AND. true = false
false .AND. false = false

Or .OR. The operator .OR. combines two logical values as follows

true .OR. true = true
true .OR. false = true
false .OR. true = true
false .OR. false = false

Not .NOT. The operator .NOT. reverses the bit configuration of a logical value. A true value becomes false and a false value becomes true.


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Numeric comparisons

Equal to .EQ. Compares one number to another for equality.
Not equal .NE. Compares one number to another for inequality.
Greater than .GT. Compares one number to another for a greater value in the first number.
Greater than or equal to .GE. Compares one number to another for greater or equal value in the first number.
Less than or equal to .LE. Compares one number to another for a lesser or equal value in the first number.
Less than .LT. Compares one number to another for a lesser value in the first number.


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String comparisons

The operators for string comparisons are the same as for numeric comparisons with an added "S" for string.

Equal to .EQS. Compares one character string to another for equality.
Not equal .NES. Compares one character string to another for inequality.
Greater than .GTS. Compares one character string to another for a greater value in the first specified string.
Greater than or equal to .GES. Compares one character string to another for greater or equal value in the first specified string.
Less than or equal to .LES. Compares one character string to another for a lesser or equal value in the first specified string.
Less than .LTS. Compares one character string to another for a lesser value in the first specified string.


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How to copy and paste using the mouse

In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.


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List of common commands

$ VUE	                            !Start the session manager. Press enter after to regain prompt.
$ DEC	                            !Open a new DEC terminal
$ UCT	                            !Open the micro-CT control panel.
$ UCT_SAMPLE	                    !Start µCT Samples.
$ UCT_MEASUREMENT	            !Start µCT Tomography.
$ UCT_EVALUATION	            !Start µCT Evaluation Program.
$ UCT_3D	                    !Start µCT Ray.
$ UCT_BACKUP	                    !Start µCT Disk-Utility.
$ CD UD	                            !Change location to the data directory.
$ CD UR	                            !Change location to the projects directory.
$ CD SYS$SCRATCH	            !Change location to the scratch directory.
$ CD UCT_RESULTS	            !Change location to the results directory.
$ DIR UE	                    !List files in the evaluation directory.
$ DIR UU	                    !List files in the templates directory.
$ DIR COM	                    !List files in the commands directory.
$ UCT_LIST	                    !Extract results from the database.
$ AIX -L	                    !View the header of an AIM file.
$ CTHEADER	                    !View the header of an RSQ or ISQ file.
$ EVE	                            !Start the text editor.
$ DISKS		                    !Show the current disk usage (all hard drives).
$ LOGOUT	                    !End a session. For remote sessions, logout from the main (initial) login terminal.

How to move to a different directory

Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path. 

$ SET DEFAULT disk:[dir.subdir]	      !Moves to specified path.
$ SET DEFAULT [.subdir]		      !Moves one level into subdirectory subdir.

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM). 

$ CD subdir	                      !Moves into subdirectory subdir.
$ CD subdir1 subdir2	              !Moves into subdirectory subdir1, then into subdir2.
$ CD ..		                      !Moves up one level (i.e., out of one directory).


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How to list the files in a directory

Use the DIRECTORY command, which may be abbreviated to DIR. 

$ DIR		                      !List everything in the current directory.
$ DIR disk:[dir.subdir]		      !Lists everything in the specified directory.
$ DIR disk:[dir.subdir...]	      !Lists everything in the specified directory and subdirectories. 
$ DIR/COL=1 *.aim	              !Lists all files with the extension .aim in a single column.
$ DIR /VERSIONS=1	              !Show only the newest version of each file in the directory.
$ DIR/SINCE=TODAY		      !Lists all files created today.
$ DIR [...*.aim]                      !The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ DIR/SIZE	                      !Lists each file and its size.
$ dir/size/grand_total [.subdir...]   !List the total size of all files in the SUBDIR directory. 
$ HELP DIR	                      !More information on the DIRECTORY command.


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How to copy files

Use the COPY or BACKUP command. 

$ COPY file1.ext disk:[dir.subdir1]file2.ext          !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1]	              !Copy all .aim files (including all versions) to another location keeping the same name.
$ HELP COPY		                              !More information on the COPY command.

$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...]      !Copy entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP BACKUP		                              !More information on the BACKUP command.


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How to delete files

Use the DELETE command, which may be abbreviated to DEL. 

$ DEL myfile.txt;	              !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;*	              !Delete all versions of myfile.txt.
$ HELP DELETE		              !More information on the DELETE command.

Warning: Extreme caution! 

$ DEL *.*;*	                      !Delete everything in the current directory!


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How to create a directory

Use the CREATE/DIR command. 

$ CREATE/DIR [.subdir]	              !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir]	      !Creates the subdirectory subdir at the specified path.


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How to rename files and directories

Use the RENAME command. 

$ SET FILE/PROTECTION=O:RWED olddir.dir         !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext                !Renames oldfile.ext to newfile.ext.


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How to check the queue

Use the SHOW QUEUE command, which may be abbreviated to SH QUE. 

$ SHOW QUEUE	                      !Shows all the queues, there are many!
$ SH QUE *FAST	                      !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW                        !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL	              !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL	      !Show only jobs that are currently executing for all users.


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How to get queue information

Use the SHOW ENTRY command to obtain information about batch jobs in the queues. 

$ SHOW ENTRY	                      !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251	              !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL                 !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL                      !Shows all the batch jobs for all users.


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How to FTP files

Use the FTP command. 

$ FTP 136.159.74.231	              !Connect to an FTP Server. Need to input user name and password.	
FTP> bin	                      !Set transfer mode to binary (.aim, .gobj, .isq, and most file types).
FTP> ascii	                      !Set transfer mode to ascii (.txt, .log, .com files).
FTP> mput *.aim	                      !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim	                      !Get all files with the .aim extension from the FTP server (mput = multiple get).
FTP> quit	                      !Disconnect from the FTP Server.


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Micro-Computed Tomography (µCT)

User Tutorial

For Scanco MicroCT Systems and Software:

For XtremeCT II and I:

For MicroCT35, VivaCT40 and VivaCT80:


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Micro-CT Image Basics

Computed tomography is a non-destructive x-ray imaging modality that enables three-dimensional (3D) virtual models of an object to be created, which can be subsequently visualized and analyzed. Micro-CT refers to CT in which the resolution lies in the micro-scale, which is achieved with a high-resolution x-ray detector and a field of view that is much smaller than conventional CT. Structural detail provided by CT depends on differences in x-ray attenuation properties. Components with very different x-ray attenuation properties, for example air, soft tissue, and bone, can be differentiated in a CT scans whereas different types of soft tissues, for example muscle and cartilage, do not have sufficient differences in attenuation to be distinguish.

Dark Field

Detector response with x-rays off. Enables corrections of non-uniformities of the detector. Acquired automatically by the scanning software before each scan.

Bright Field

Detector response with x-rays on but no sample. Enables corrections of non-uniformities of the x-ray beam. Acquired automatically by the scanning software before each scan.

Raw Projection

A raw x-ray projection of a mouse leg. The darker regions correspond with higher x-ray attenuation. The discontinuities result from overlaps where the detector was shifted to acquire the large region of interest (3x2 detector frames in this example). Projections are acquired at many incremental rotations around the sample.

Sinogram

The sinogram is a different representation of the projection data. The sinogram represents the attenuation values of one row of the detector at each rotational increment around the sample.

Attenuation Projection

Accounting for the inhomogeneities of the detector and beam, we can calculate the x-ray attenuation caused by the sample. Bright regions correspond with higher attenuation.

Reconstructed Image

From the attenuation projections, the original structure can be calculate using filtered back projection.


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Image Data Type

Binary Images

Binary images are images whose pixels contain only two possible intensity values (off-on, or black-white B&W). The off or black value is usually 0 and the on or white value is usually 1 (1-bit pixel) or 255 (8-bit pixel). This type of image is commonly used as a multiplier to mask regions within another image.

Grayscale Images

Grayscale images represent intensities. Pixels range from least intense (black) to most intense (white). Pixel values usually range from 0 to 255 or are scaled to this range when displayed.

Indexed Images

An indexed image uses direct mapping of pixel values to colormap values. Instead of intensities, a pixel value within an indexed image relates to a color value within a color lookup table. An indexed image consists of a data matrix and a colormap matrix. The data matrix can be of class uint8, uint16, or double. The colormap matrix is an m-by-3 array of class double containing floating-point values in the range [0,1]. Each row of map specifies the red, green, and blue components of a single color. Since indexed images reference color tables composed of up to 256 colors, the data values of these images are usually scaled to range from 0 to 255.

RGB Images

Within the three-dimensional array of an RGB image, two of the dimensions specify the location of a pixel within an image. The other dimension specifies the color of each pixel. The color dimension always has a size of 3 and is composed of the red, green, and blue color bands (channels) of the image.


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Pixel Values in Image Data

The image data type is determined by the pixel depth in bits per channel, or bit depth. Bit depth for each channel can be 8, 16, 32 or 64. The data may be signed, unsigned (u), floating-point (f), real or complex (c) for some arithmetic functions, where each channel value is represented by two numbers: real and imaginary part. All channels in an image must have the same data type.

Image Data Type Name Byte Value Range Comments
char 8-bit signed integer 1 -128 ~ 127 Scanco SEG.AIM, GOBJ
uchar 8-bit unsigned integer 1 0 ~ 255
int 16-bit signed integer 2 −32768 ~ 32767 Scanco grey-scaled images, ISQ, AIM
uint 16-bit unsigned integer 2 0 ~ 65535 Converted format of Scanco grey-scaled images
long 32-bit signed integer 4 −2^31 ~ 2^31 - 1
ulong 32-bit unsigned integer 4 0 ~ 2^32 - 1
float floating point 4 ±3.40282347 E+38 32-bit single-precision with 6~7 significant digits
long64 64-bit signed integer 8 −2^63 ~ 2^63 - 1
ulong64 64-bit unsigned integer 8 0 ~ 2^64 - 1
double double precision floating point 8 ±1.79769313486231570 E+308 64-bit double-precision with 15~16 significant digits
complex floating point complex 8 same as floating-point same as floating-point
dcomplex double precision complex 16 same as double-precision same as double-precision


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Scanco Medical Micro-CT Software

In the bottom left hand corner of the micro-CT workstation desktop is the micro-CT control panel, from which the micro-CT programs can be launched. The standard operating procedure for scanning a samples involves proceeding through the programs in the control panel from left to right: 

$ UCT_SAMPLE         !Samples:      Registering a sample
$ UCT_MEASUREMENT    !Tomography:   Scanning
$ UCT_EVALUATION     !Evaluation:   Evaluating the scan
$ UCT_3D             !Ray:          Viewing the 3D scan
$ UCT_BACKUP         !Disk-Utility: Archiving the data

You must specify an operator in the control panel to use the scanning and evaluation programs.

  • XtremeCT

  • MicroCT35, VivaCT40 and VivaCT80


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µCT Samples

The µCT-Samples program is used to register new samples to be scanned and update sample names (e.g., to correct a sample name). To start the program type $ uct_sample in a DEC terminal, or use the sample button.

  1. Prepare Sample Names according to Sample Name Convention
  2. Register Sample Names
    • Create a new sample by clicking “New” and typing in your sample name where it says “Name.” “Save” the sample.
    • You are now given a sample number. Record the sample number on the log sheet.
  3. Create Additional Sample Names Using Copy and Paste
    • If you have many samples to register, you can copy and paste part of the sample name you just created. Highlight the part of the sample name you want to copy by holding down the left mouse button while dragging the mouse, then release the mouse button.
    • Paste the highlighted text into a DEC terminal by pressing the middle mouse button. Now highlight the text in the DEC term.
    • Go back to the µCT-sample window, click "New", and paste the information next to "Name" using the middle mouse button. Update the name as required and "Save."
  4. Add Additional Sample Details
    • When a patient comes in for their first scan, you need to update their sample with their date of birth, sex, and hand/foot dominance.
    • Use the "Find..." button to search for a sample that has already been registered. You can search by sample number or by project name (e.g., CAMOS).
    • Date of birth: DD/MMM/YYYY
    Example: 14/JAN/1951
    • Sample remarks: include the sex and hand/foot dominance
    Example: F-RHRF for female that is right hand dominant and right foot dominant


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µCT Tomography

The µCT-Tomography program is used to perform a scan. To start the program type $ uct_measurement in a DEC terminal on the scanner computer (remote access does not allow this functionality), or use the scanner button. If you use the button, you must specify an operator prior to using the program.


  1. Select Sample
    • When the µCT-Tomography program is first started, you will be prompted to enter the sample name or number of the specimen you are about to scan.
    • If you have not registered your sample, press "Cancel" to close the select sample box, then press "New..." in the measurement sample box to register a new sample (see µCT-Samples).
    • Once you have entered your sample information, the measurement sample box will show details for that sample, including the sample name and scan (measurement) history.
    • After your first scan you will need to press the "Other..." button to open the sample selection box and find your next sample.
  2. Select a Controlfile
    • The controlfile contains scan parameters such as the x-ray energy, current, and more (see Controlfiles).
    • Once the controlfile is setup, you need only to select it. If there are many controlfiles, you may want to search for yours using the file filter by entering part of the name or number in the white box and pressing enter; if you do this, you still must click on the controlfile so that it is highlighted in black as shown below.
  3. Precalibrate
    • Calibrations are done before loading your patient/animal and scanning for quality control and to reduce the time the patient/animal is under preparation/anaesthesia. Start the calibration by pressing the "Precalibrate" button.
    • Press "Start Calibration". The calibration will start with an "X-Ray Warmup", followed by "Measuring Dark" and "Measuring I0" and usually takes about 2-3 minutes to complete.
    • The precalibration is good for 15~20 min. The time remaining is shown on the "Precalibrate" button.
    • The precalibrate option cannot be used with batch measurements, and it's not available for MicroCT35 which is not intended for invivo/live scan.
  4. Load and Position the Patient/Sample
    • Instruct the patient to remove any jewelry in the scan areas (wrist/ankle/knee/elbow ect). With the patient seated, put the wrist/ankle/knee/elbow into the appropriate cast. Different pads with different sizes can be used to fit the patient.
    • For invivo/invitro samples, prepare your sample in terms of orientation, immobilization, hydration ect.
    • After the precalibration is complete, you can now open the bore cover and insert the patient's wrist/ankle/knee/elbow or sample into the scanner. Gently move the wrist/ankle/knee/elbow or sample into the scanner until you can snap in the cast at the gantry. Check that the cast is positioned correctly and the patient/sample is comfortable.
    • Close the bore cover.
  5. Scout-View
    • A scout-view is similar to a 2D x-ray image and allows the user to set where to start and stop the scan.
    • After loading your sample, press the "Scout-View..." button to bring up the scout-view window.
    • The start position (top of the scanner) and end position (bottom of the scanner) can be modified to zoom in on the region of interest.
    • The angle of the scout view can also be changed to see the object in a different orientation.
    • Once pressed the "Scout-View" button but the scout view is found not in an appropriate position, press "Cancel", modify the start position, end position, or angle and press "Scout-View" again.
    • Scout view image is displayed in the top right hand corner of the program and will start by showing the right half of the image, followed by the left half of the image.
  6. Set Reference Line and Launch a Scan
    • A reference line (solid green line) is placed to set the scan region (green block).
    • Press the "Reference-Line" button to show the reference line and default scan region over the scout view.
    • To change the number of slices to scan, move the reference line to the top of the scan region, then hold down the shift button while dragging the mouse to extend the scan region and press the left mouse button to set the reference line.
    • To centre the scan region between two reference lines, move the reference line to the top of the scan region, then hold down the alt key while dragging the mouse until the second green reference line is in place, then press the left mouse button to set while still holding down the alt key!
    • For a single scan, select "OK", "Scan" and "Start Measurement". Record measurement number on your log sheet.
    • For a batch scan which is only available on microCTs, select "Batch Measurement" and record the measurement number on your log sheet. You may now setup a new scan (select new sample and controlfile, perform scout, etc). When you have finished setting up all scans, press "Start Batch Scans." (See Perform Batch Scans for detailed instructions)
  7. Cancel or Reposition a Scan
    • If you need to interrupt a scan, press the cancel button and restart the scan or if you do not want to rescan then "unload" the scanner.
    • If you have not started a scan and need to reposition the patient, you also must "unload" the scanner.
  8. Remove Patient/Sample from Scanner
    • After the scanning is complete, open the bore cover and slide the patient's wrist/ankle/knee/elbow or sample out of the scanner. Release the cast by pushing down the cast release handle.


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µCT Evaluation Program

The µCT Evaluation Program is used to evaluate a scan. To start the program type $ uct_evaluation in a DEC terminal, or use the graph button. If you use the button, you must specify an operator prior to using the program.


  1. Find Your Sample
    Enter the first part of your sample name in the file filter box and press enter. The samples are shown in the left hand box. The measurement box on the right shows scans for the selected sample (highlighted in black). Select a measurement and press "OK."
  2. Draw Contours (If Applicable)
    • Contours, or GOBJ files, are drawn to define regions of interest. Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).
    • Contours must always be drawn COUNTER-CLOCKWISE!!!
    • Contouring tools reference sheet
    • For this sample, we are only interested in viewing the object in 3D and drew contours to isolate the bone and soft tissue from the sample tube.
  3. Evaluate
    • Scanco Medical provides several standard evaluation scripts. Open the 3D-Evaluation menu either using the "T..." button or from the top menu by going to "Tasks" and "Evaluation 3D...". If you set a default evaluation script in your scanning controlfile, it will be listed under "Task/Evaluation."
    • If you want to run a different evaluation press "Select...", highlight the evaluation script of interest, and press "OK".
    • When the 3D-Evaluation window is activated, a white box will appear on your reconstructed image. The white box is the region of interest that will be "cut out" of the full scan. If you have drawn contours, the white box will automatically be adjusted to fit the contours. Adjust the box if necessary by grabbing one of the white handles; use the left mouse button to move the box and the right mouse button to resize. The box can also be resized using the "VOI Start" and "Dimensions" in the 3D-Evaluation window.
    • For most evaluation scripts, you will be required to specify parameters for a Gaussian filter, to reduce noise, and a threshold, to isolate your object (e.g., bone) from the background. Check that the parameters used provide a good representation of your scanned sample by flipping back and forth between the segmented and grayscale image using the "Preview" and "Grayscale" buttons.
    • When you are satisfied with the segmentation parameters, press "Start Evaluation", which will submit the job to the queue.


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µCT Ray

The µCT Ray program is used to view scanned objects in 3D, create images, and create image sequences for animations. To start the program type $ uct_3d in a DEC terminal, or use the 3D object button.


  1. Select and Render Your Sample
    • Select: If you have used the default Scanco Medical scripts, then search for your files using the file filter to select a sample and measurement then press "OK".
    • Rendering: Use a single click of the left mouse button to start or to stop rendering the sample. You can also use the "Start" and "Stop" buttons at the bottom of the options on the left. You must stop rendering to change viewing options on the left.
    • Change the View: To adjust the view, move the "Rotation" and "Elevation" slider bars in the options on the left. Note, the slider bar is located above its label.
    • Change Colours (Object and Background): From the top menu choose "Options" then "Object/Display Properties...". A segmented image typically only has two values, 0 (black, background) and 127 (white, object). To change the colour of the object only, we need to set the value 127 to a specific colour. In this example, the slider bar value "1" corresponds with the value 127 and we will set both slider bars to "1" so that we are adjusting values "127 ... 127", in other words, only value "127".
    Under "Surface" click on the "white box" to open the "Color Mixing" window. Choose the new colour for the object (e.g., orange) and press "OK." Close the "Object Properties" window or move it to the side. Now re-render the object with a single click of the left mouse button.
    • Cutplane (left options) and Subdim (top menu): The cutplane and subdim functions allow you to show a cross-section of your object. The subdim function tends to work better than the cutplane but is limited to axes of the scan.
  2. Print an Image to File
    An image must be fully rendered in order to be saved. From the top menu choose "File" then "Print". Set the print format to "TIFF" and the directory to "Scratch/Temp" (or another location using the "Specify in Filename" option). Change the filename to something meaningful then press "OK."
  3. Auto-Print Images for an Animation
    • Creating an animation involves saving a sequence of rendered images, which can then be compiled into an animated GIF or other video format using various software packages (e.g., Photoshop, Quicktime Pro).
    • From the top menu choose "Options" and "Animation..." to open the Animation Settings window. Set the viewing parameters for the start of the animation, fully render the image, then press the "Get Settings A" button.
    • Set the parameters for the end of the animation, fully render the image, then press the "Get Settings B" button.
    • Set the number of frames you want, the higher the number frames, the smoother the animation will be, but also the larger the file size.
    • Now setup the auto-print feature. From the top menu choose "File", then "Print". Choose "TIFF" for the print format, and the "Scratch/Temp" for the directory (or use the "Specify in Filename"). Specify a filename prefix, to which numbers will be appended for the image sequence.
    • Activate the "Auto-Print" feature. Press "OK" then press the "Start Calculation" button on the Animation Settings window.
    • Do not interrupt the program while the frames are being rendered and saved. When the program is done rendering all the frames, transfer them to your computer to compile into an animation.


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µCT Disk-Utility

The µCT Disk-Utility Program is used to archive and restore scan data. To start the program type $ uct_backup in a DEC terminal, or use the disk button.


  • Tape Label Convention

Tape labels are 6 characters in length. The first two characters are set to your PI's initials, the third character indicates if the tape is for raw (R) or image (I) data, and the last three digits are for the tape number. 

SBR040 = Steve Boyd RAW, tape #040 <br>
SBI001 = Steve Boyd IMA, tape #001 <br>
BHR006 = Benedikt Hallgrimsson RAW, tape #006 <br>
BHI017 = Benedikt Hallgrimsson IMA, tape #017 <br>
FJR012 = Frank Jirik RAW, tape #012 <br>
FJI003 = Frank Jirik IMA, tape #003 <br>

When a tape becomes full, start (initialize) a new tape, increasing the tape number by one so that each tape label is unique.


  • Initialize a New Tap

Put a new tape into the tape drive, then press "Initialize", this will format (erase) everything on the tape. When prompted for a label for the tape, follow the Tape Label Convention. The tape can now be mounted for use.


  • Full Tape

A tape automatically ejects during a backup procedure if it becomes full. Remove the tape and write protect it (orange indicator will be displayed). Exit the disk-utility program. Start a new instance of the program. Initialize a new tape. Backup any remaining files.


  • Archive and Backup procedure
  1. Backup RAW Data (1-2 days after scanning)
    • RSQ files are backed up onto RAW tapes (see Tape Label Convention). Put the most recent RAW tape into the tape drive, then press "Mount".
    • Show "Current (with RAW)", type in the beginning of your sample names (e.g., BUIE) in the file filter and press enter or press "Update List".
    • Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
    • Highlight RAW, choose "Move To" and "Tape". Press "Start...".
    • When the backup is complete press "Dismount" to eject the tape.
    • If the tape auto-ejected without pressing "Dismount" then the tape is full (see Full Tape).

  2. Delete ISQ After Evaluation (variable, ideally 1-2 weeks after scanning)
    • ISQ files are normally deleted after completing your evaluation since they are very large files and can be reconstructed from the RSQ file.
    • Show "Current (on Disk)", type in the beginning of your sample names (e.g., MANSKE) in the file filter and press enter or press "Update List".
    • Select all the files for which you have completed the evaluation (there will be a + sign next to any scan that has been evaluated). #*Highlight IMA, choose "Move To" and "Trash".
    • After you choose the trash symbol, you will now be given the option to select specific file types, choose "Select" and "ISQ". Press "Start...".

  3. Backup IMAGE Data (variable, ideally 1-2 weeks after scanning)
    • AIM, GOBJ and other evaluation files are backed up onto IMA tapes (see Tape Label Convention).
    • Put the most recent IMA tape into the tape drive, then press "Mount".
    • Show "Current (on Disk)", type in the beginning of your sample names (e.g., MANSKE) in the file filter and press enter or press "Update List".
    • Select all the files to backup by highlighting them using the left mouse button and ctrl to select individual files or shift to select a range.
    • Highlight IMA, choose "Move To" and "Tape". Press "Start...".
    • When the backup is complete press "Dismount" to eject the tape.
    • If the tape auto-ejected without pressing "Dismount" then the tape is full (see Full Tape).


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XImage

The XImage program is used to view the raw data (RSQ file) and scout view. To start the program type $ run um:ximage in a DEC terminal.

When loading an RSQ, the default view (XY plane) is of the sinogram.

To view the attenuations, choose the XZ plane. The first slice in this orientation is the dark field, the second slice is the bright field , and slices three and onward are the attenuations.

To view the corrected projections, from the Evaluations menu, choose Projection Mode.


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Scanning

Sample Name Convention

  • At the Bone Imaging Laboratory, all sample naming must conform to the following format
PROJECT IDENTIFIER _ SAMPLE DETAILS
  • In CAPITAL LETTERS (filenames are case sensitive, so this makes it easy to remember how you input your sample name)
  • No special characters (spaces, /, %, etc.) as further evaluations will not work if spaces are present.
Examples: CAMOS_771, TESTS_0001, TESTS_0002, TESTS_0003

Register Samples for Scanning

  • Although samples can be registered immediately prior to a scan, it is much more efficient to register all your samples beforehand.
  • Refer to µCT Samples for instructional details.

Log Sheets

  • Log sheets are used to record important information about scans that are performed, such as sample and measurement numbers ect.
  • Log sheets are to remain in the lab. If you would like a copy of your log sheets, please make a photocopy or print two copies to record the scan information.
  • Use the PDF file to print blank log sheets. Use the Excel file to make your own custom log sheet.
  1. Bone Lab for General Patients
  2. MicroCT Lab for General Non-Patients


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Sample Holders and Patient Casts

Patient Casts for XtremeCTs

Sample Holders for microCTs

Ex Vivo Sample Holders

  • Ex vivo and inanimate samples are scanned in sample holder tubes. These tubes come in a variety of diameters. It is extremely important that the tube diameter corresponds to, or is smaller than, the field of view (FOV) set in your scanning control file.
  • Biological tissues should be hydrated and wrapped in plastic wrap to prevent drying of the sample. Your sample should then be secured in the sample holder using foam to prevent it from shifting around during scanning, which would lead to poor image quality.
Chemical Resistivity of Sample Holders
  • White tube sample holders are made of PMMA (poly-methyl-methacrylate).
  • Yellow tube samples holders are made of PEI (poly-ether-imide).
  • Use the yellow tubes if you will need to disinfect the sample holder after scanning.
Thermal and chemical compatibility of sample holders
Properties White Tubes (PMMA) Yellow Tubes (PEI)
Max. Temperature +85°C +170°C
Sterilization Steam Autoclave non resistant resistant (138°C for 20 Min. at 1 bar)
Water resistant resistant
Inorganic Acids limited resistance resistant
Inorganic Bases non resistant limited resistance
Aldehydes (Formaldehyde) limited resistance only in diluted form resistant
Alcohols limited resistance resistant
Bleach non resistant resistant
Mounting of Sample Holders
µCT35 setup
  • The spindle (metal bit) of the sample holder has a slot, which must be aligned in the scanner or adapter plate.
  • The sample holder sits vertically in the µCT35 while horizontally in the VivaCT80 and VivaCT40.
  • For the vivaCT40, attach the adapter plate for the tube sample holders to one of the animal bed. The tube sample holders are held horizontally in the vivaCT 40.
VivaCT40 setup


In Vivo Sample Fixtures and Anesthetic System


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Scan Parameters (Controlfiles)

Controlfiles are used to specify the parameters for the scans. Once your controlfile is setup, you should not modify it over the course of your project.


  • Control File Name: Specify a meaningful name so that others can reuse yours.

General Settings

  • Holder Type: Choose the used holder type for XtremeCT II from Standard Casts, Knee Cast and Elbow Cast. No option for XtremeCT I scanner. For microCTs, Choose the used sample holder type with the correct diameter.
  • Mode of operation: Default is continuous operation for all scanners. Gated operation mode is available for VivaCT80 and VivaCT40 scanners.
  • Evaluation Script: This sets the default evaluation script used for the analysis. You can manually select a different script from the evaluation program.

X-ray Settings

  • Tube Energy (KVp): Fixed energy for XtremeCTs while having 3 options for each of microCTs: Use the 70 KVp for most samples, use the 55 or 45 KVp for low density objects (e.g., soft tissue) or specimens with a diameter less than 20 mm. Lower energies provide better contrast while higher energies provide better signal to noise (SNR).
  • Tube Current (µA): Fixed current for XtremeCTs while having 2 options for each of energy settings of each microCTs: Use the higher current except when the voxel size is set for the best resolution of the scanner. The higher current will yield better SNR but a larger spot size.
XtremeCT II XtremeCT I vivaCT80，vivaCT40， µCT35
E (KVp) 68 60 70 55 45
I (µA) 1470 900 114, 57 145, 72 177, 88
Power (W) 100 54 8, 4 8, 4 8, 4
  • Filter: Fixed filter settings for all scanners except VivaCT 80 has 4 filter options.
XtremeCT II XtremeCT I vivaCT80 VivaCT40 µCT35
Filter Fixed 0.2 mm Cu + 1 mm Al

(Equivalent 6.7 mm Al)

Fixed 0.1 mm Cu + 0.6 mm Al Default 0.5 mm Al,

Air, 0.1 mm Al, 0.1 mm Cu

Fixed 0.5 mm Al Fixed 0.5 mm Al
  • Calibration: This sets the mu scaling factor, density and beam hardening correction used for the reconstruction. For standard patient scans use 200 mg HA/cm3. For ex vivo bone scans, use 1200 mg HA/cm3, for soft tissue use the plexi scaling, and for non-biological tissues use the aluminum scaling.


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Scout-View Settings

Normally you will want to enable this and here you can specify the default start and end position, and scout-view angle, which you may override for each scan.

CT Scan Settings

  • Resolution: This setting includes the reconstruction matrix size (2048x2048, 1536x1536, 1024x1024, or 512x512) and the number of projections per 180°. The lower the resolution setting, the better the SNR and larger the voxel size.
  • FOV / Diameter: This field of view must fully contain the sample holder for accurate density measurements. Fixed FOV for XtremeCTs while having 5 options for each of microCTs: If you choose a smaller FOV than the sample holder, the scan may be aborted to prevent damage to the scanner. For the best resolution, you should choose the smallest holder that contains your sample.
  • Voxel Size: The nominal isotropic voxel size is determined by the FOV and the reconstruction matrix.
XtremeCT II XtremeCT I vivaCT80 VivaCT40 µCT35
FOV (⌀ * L mm^2) 140 ⌀ * 200 L 126 ⌀ * 150 L 31.9 ~ 80 ⌀ * 145 L 21.5 ~ 38.9 ⌀ * 148 L 7.2 ~ 38 ⌀ * 140 L (75 L standard)
Image Matrix 4608*4608 ~ 512*512 3072*3072 ~ 512*512 4096*4096 ~ 512*512 2048*2048 ~ 512*512 2048*2048 ~ 512*512
Voxel Size (µm) Standard 60.7 (30.3 ~ 273.4) Standard 82.0 (41.0 ~ 246.0) 5 ~ 156 10.5 ~ 76 3.5 ~ 74
  • Number of Slices: You can specify a specific number of slices or image stacks to acquire (1x110 = 1 image stacks of 110 slices). The scan time increases with each image stack, therefore pay attention to the stack boundaries (e.g., 111 slices will take 2x longer to scan than 110 slices).
  • Rel Position of First Slice: This option enables you to offset the scan region from the reference line. This is useful for scanning a region a specific distance from the growth plate or centering the scan region around the reference line. If you disable the scout view, then the position is relative to the absolute 0 position of the scanner (top of the sample holder for the µCT35 and towards the back of the scanner for the vivaCT40).
  • Integration Time: The higher the integration time, the better the SNR and longer the scan time. Use 100 ms for patient scans and higher values for ex vivo scans of better image quality. To get the highest integration time, uncheck the "Continuous ROT" button. For standard microCT measurements, use ~400 ms for the µCT35 and ~200 ms for the vivaCT40. The maximum integration time is scanner-specific and limited to prevent saturation of its detector.
  • Average Data: This is often referred to as frame averaging and is used to improve a scan's SNR. Multiply the average data value by the integration time to calculate the effective integration time. Only use this if the integration time is maxed out.
  • Measurement Time: This is the estimated scan time without the time performing the scout view or warm-up of the scanner.
  • CTDIvol: Computed Tomography Dose Index (CTDI) is a standardized measure of radiation dose output of a CT scanner for scanner settings' comparison purposes only, and it represents the average absorbed dose along the longitudinal axis from a series of contiguous CT exposures. Volumetric CTDI is the ratio of the weighted-CTDI to the level of overlap between slices (pitch). CTDIvol has no consideration of real scan length and does not represent actual dose administered to the patient.
  • DLP: Dose Length Product DLP = CTDIvol * Scan Length in unit of mGy-cm.


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XtremeCT II Scan Settings

Resolution Choice Native Custom High Medium Standard
Image Matrix 4608 2304 1536 1024 512
Projection/180° 3000 900 750 500 250
Voxel Size (µm) FOV/Diameter 140 mm 30.3 60.7 91.1 136.7 273.4
Slices/Stack 338 168 112 74 37
Stack Thickness (mm) 10.24 10.20 10.20 10.12 10.12
Time/Stack (min, at 43 ms Integration Time) 8.1 2.0 2.0 1.4 0.7
Time Current Product (mAs) 238 71 59 40 20
CTDIvol (mGy) 37.4 11.2 9.3 6.4 3.2
DLP (mGycm) 38.3 11.4 9.5 6.4 3.2

XtremeCT I Scan Settings

Resolution Choice Custom High Medium Standard
Image Matrix 3072 1536 1024 512
Projection/180° 1000 750 500 250
Voxel Size (µm) FOV/Diameter 126 mm 41 82 123 246
Slices/Stack 221 110 73 36
Stack Thickness (mm) 9.06 9.02 8.98 8.86
Time/Stack (min, at 100 ms Integration Time) 3.7 2.8 1.9 1.0
Time Current Product (mAs) 114 86 57 29
CTDIvol (mGy) 7.3 5.5 3.6 1.9


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VivaCT80 Scan Settings

Resolution Choice Native High Medium Standard Custom
Image Matrix 3072 2048 1024 1024 512
Projection/180° 1500 1000 500 250 125
Voxel Size (µm) FOV/Diameter 31.9 mm 10.4 15.6 31.9 31.2 62.4
FOV/Diameter 35.9 mm 11.6 17.5 35 35 70.1
FOV/Diameter 39.9 mm 13 19.5 39 39 78
FOV/Diameter 49.8 mm 16.1 24.2 48.5 48.5 97.1
FOV/Diameter 63.9 mm 20.8 31.2 62.4 62.4 124.8
FOV/Diameter 79.9 mm 26 39 78 78 156
Slices/Stack 333 ~ 328 222 ~ 219 111 ~ 109 111 ~ 109 55 ~ 54
Time/Stack (min, at 200 ms Integration Time) 14.9 10.0 5.0 2.5 1.3
Time Current Product (mAs) 73 48 24 12 6

VivaCT40 Scan Settings

Resolution Choice High Medium Standard Custom
Image Matrix 2048 1024 1024 512
Projection/180° 1000 500 250 125
Voxel Size (µm) FOV/Diameter 21.5 mm 10.5 21 21 42
FOV/Diameter 25.6 mm 12.5 25 25 50
FOV/Diameter 30.7 mm 15 30 30 60
FOV/Diameter 35.8 mm 17.5 35 35 70
FOV/Diameter 38.9 mm 19 38 38 76
Slices/Stack 213 106 106 53
Time/Stack (min, at 200 ms Integration Time) 9.9 5.0 2.5 1.3
Time Current Product (mAs) 61 31 15 8

µCT35 Scan Settings

Resolution Choice High Medium Standard Custom
Image Matrix 2048 1024 1024 512
Projection/180° 1000 500 250 125
Voxel Size (µm) FOV/Diameter 7.2 mm 3.5 7 7 14
FOV/Diameter 12.3 mm 6 12 12 24
FOV/Diameter 20.5 mm 10 20 20 40
FOV/Diameter 30.7 mm 15 30 30 60
FOV/Diameter 37.9 mm 18.5 37 37 74
Slices/Stack 232 ~ 235 116 ~ 117 116 ~ 117 58
Time/Stack (min, at 400 ms Integration Time) 23.9 12.3 6.5 3.5
Time Current Product (mAs) 119 60 30 15


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Advanced Settings

  • Number of Det-lines (for Scout-View): Defines how many lines on the detector shall be used during the Scout-View. Using all available lines provides faster Scout-Views but some faint horizontal lines might be seen between the stacks. Limit the number of lines to a small number to obtain Scout-Views without these artifacts but the time of the Scout-View will increase.
  • Number of Det-lines (for CT-scan): Defines how many lines on the detector should be used. This number influences the number of slices within a stack. Limit the number of detection lines if you see residual cone beam artifacts.
  • FOV/Scan Diameter: Chose the diameter of the FOV. This action is cropping the area of the detector.
  • Software binning: factor of the pixels on the detector.
  • Hardware binning:
  • Samples: number of (possibly binned) pixels on the detector that are used for each slice (note: this number is given for the whole FOV).
  • Proj/180°: number of projections taken per 180° turn of the sample.

Reconstruction

  • After each image stack is acquired, it is automatically submitted to the queue (sys$slow) for reconstruction. The reconstruction for each image stack is split into four jobs to make efficient use of processors.
  • The reconstruction time depends on the resolution setting, with low resolution scans reconstructing faster than high resolution scans. Normally scans are reconstructed within a day or two.
  • It is possible to resubmit a scan for reconstruction; this may be necessary or desireable for several reasons:
  1. The sample did not reconstruct properly (e.g., due to a power failure)
  2. To reconstruct the object at an angle (e.g., so that the anterior surface of a bone is always in the same direction).
  3. A new beam hardening correction was applied to the sample
  4. The scaling was changed for the sample to change the brightness


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Perform a Scan

Perform a Single Scan

Perform Batch Scans

  • Batch scan mode is only available on microCT scanners.
  • Batch scans can be setup for different regions of interest (ROI) within a sample or for different samples contained within a sample holder.
  1. Setup the First Scan
    • Refer to µCT Tomography to use the "Other..." button to find your sample number, choose a controlfile, perform a scout view (a mouse's whole body in this example), use the reference line to setup the first scan region (mouse skull in this example).
    • To add a batch scan press the "Batch Measurement" button.
    • An information window is displayed with the scan measurement number. Record the measurement number on your log sheet then press "OK" to close the window. An entry is also added to the measurement history for the sample.
  2. Setup the Next Scan
    • Using the "Other..." button, find your next sample number, choose a new control file (if desired).
    • If the next region of interest or sample is not in view of the current scout view, adjust the parameters of the scout view and obtain a new one.
    • Use the reference line to set a new scan region (upper limbs in this example).
    • To add a batch scan press the "Batch Measurement" button.
    • As the first scan, a measurement number is assigned for this new scan. Record the measurement number on your log sheet.
    • Repeat this process until you have added all your scans.
  3. Start the Batch Scans
    There are two ways to start a batch scan:
    1. Click the "Start Batch Scans" button: the program will automatically close so that control of the scanner can be allotted to the queue.
    2. Exit the scanning program.
  4. Check the Queue
    • Batch jobs will be submitted to the SCEVA2_BATCH queue for µCT35 or SC5019_BATCH queue for vivaCT40.
    • Initially the jobs will show up as temporary (TMP) jobs:
    • After about 30 seconds, the sample number will show up in entrie names:
  5. Request an Email Notification
    • There is a script in the commands (com) directory that will put an entry into the batch queue to send an email. Run the script and input parameters (queue and email) as prompted.
  6. Cancel a Batch Scan
    • For errors made during batch scan setup, to cancel a scan in progress, or to cancel a pending scan.
    • If you cancel all the scans and the scanner door does not unlock automatically (µCT 35 only), then start the measurement program and the scanner will unload, unlocking the door.


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Image Artifacts

Rescan for

  • Motion Artifacts
  • Sample Out of the Field of View

Contact Scanco Medical for

  • Ring Artifacts (Bad Detector)
  • Ring artifacts are caused by a faulty detector pixel and show up in the reconstructed image as a full or partial white circle.
  • When noticed, please notify lab technicians who will contact Scanco Medical to perform a "Pixel Correction", which will correct this artifact for future scans and can be used to update previous scans.
  • You should not rescan the sample if there is a ring artifact.
  • Image with Ring Artifact
  • Same Image after with Detector Correction
  • Bad Centre Calibration Values
  • Defective Shutter Artifact


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Evaluation

Open default ISQ

Can’t open the ISQ in uct_evalution??? Modify the database, or define the default isq: 

$ def uct_default_isq dk0:[microct.data.00004111.00009899]C0007655.isq
$ uct_evaluation

Click cancel when the program opens to load the isq.


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Results

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Backup and Deletion

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Remote Access

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