Scanco User Instructions

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.

• OpenVMS Beginner's FAQ

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 XtremeCT II and I:

• Scanco XtremeCT I SOP (Berlin)

For MicroCT35, VivaCT40 and VivaCT80:

• MicroCT User Policy & Guidelines
• MicroCT Starter Package
• MicroCT Customer Training Guide

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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.

• CT Back-projection Reconstruction
• CT Reconstruction of a Head

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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

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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 (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 for more information).
   • 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 here for information on 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.

   

   • MicroCT35 doesn't have this option of Precalibration as it's not intended for invivo/live scan.
   • 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 20 min. The time remaining is shown on the "Precalibrate" button.

   

   • The precalibrate option cannot be used with batch measurements.
4. 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.
5. Reference Line
   • 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, 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." Batch jobs will be submitted to the SCEVA2_BATCH queue.

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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.)

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
   • XCT II Log Sheet for Studies
   • XCT II Log Sheet for Miscellaneous
2. MicroCT Lab for General Non-Patients
   • MicroCT Log Sheet for Studies (PDF)
   • MicroCT Log Sheet for Studies (Excel)

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Scan Parameters (Controlfiles)

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Evaluation

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