Contact email: pcmd.microct@gmail.com

Website: https://www.med.upenn.edu/orl/uct

MicroCT Core Online Training

Before Proceeding

Please finish the following before proceeding:

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• Attend the required online Cabinet X-Ray Training (https://ehrs.upenn.edu/radiation-safety/topics/radiation-safety-training), and forward confirmation email to us.

(Note: Select "4. X-Ray Training", and then select "Cabinet X-ray Units" for online training)

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• Fill in the Google Form for new user registration

https://docs.google.com/forms/d/e/1FAIpQLSf9FIFJ4krT4yNISKvWKesecFCoBxdri62wI6JlaDPIgUsCHA/viewform

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Introduction: Basic Principle

1. X-rays transmits through the sample, and recorded by the X-ray detector.
2. The sample is rotated while the X-ray projection images are taken.
3. The X-ray projection images is then computed through the process called “reconstruction”, further processed into 3D models.

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Ref: https://www.microphotonics.com/what-is-micro-ct-an-introduction/

Introduction: Ex vivo scan vs. In vivo scan

• Ex vivo (Latin for out of living) scan: Tissues from dead animals.
• During ex vivo scans: the sample will rotates (figure below), while the X-ray generator & detector remain stationary.

• In vivo (latin for within life) scan: Scanning of live animals
• During In vivo scans: The live animal remains stationary, while the X-ray generator & detector will rotate. �(opposite with ex vivo scans)
• Note: In vivo scan on live animals requires IACUC approval.

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Ref: https://www.microphotonics.com/what-is-the-difference-between-in-vivo-micro-ct-and-ex-vivo-micro-ct-scanning/

Introduction: Ex vivo vs. In vivo scanner

• We have 2 ex vivo scanners (µCT 35, µCT 45) in 335A Stemmler.

• We have 1 in vivo scanner: vivaCT 80 in 368B Stemmler.

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For more info, please visit: https://www.med.upenn.edu/orl/uct/facilities.html

Before Your Scan: Calendar of µCT Scanner

Make reservations on Google Calendar of Scanner before use!

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Calendars of µCT 35 :

• Working hours on µCT 35 are defined as: Weekdays 9am - 9pm. �Limit: 6 hours per lab per day during working hours: 9am-1pm, 1-5pm, 5-9pm.
• No restrictions on your scan day. You can reserve if additional time is available.
• No restrictions for off-hours (<9am or >9pm), weekends, and holidays.

Examples of working hours reservation:

1. If your scan takes 4 hours, you may book either 9am-1pm, or 1-5pm, or 5-9pm. You booking should NOT cross 2 time slots above, e.g.: 10am-2pm or 2-6pm.
2. If your scan takes 6 hours, you may book either 7am-1pm or 5-11pm. You may NOT book 1-7pm or 9am-3pm.
1. No restrictions on the scan day. You may extend your reservation as you wish.
2. Do NOT reserve the entire overnight as there might be early morning users.
3. In vivo scanning has priority and no reservation restrictions.

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Before Your Scan: Calendar of µCT Scanner

Make reservations on Google Calendar of Scanner before use!

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Calendars of µCT 45:

• Weekdays Limit: 24 hours continuous scan per lab.
• No restrictions on the scan day. You can reserve if additional time is available.
• Weekends & Holidays Limit: 24 hours continuous scan.

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Calendars of VivaCT 80:

• In vivo scan has priority. Currently, no reservation restrictions.

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Before Your Scan: PPE & Safety Policies

• During the pandemic, facial masks MUST be worn at all times.

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• Lab coat, safety glasses/goggles and gloves MUST be worn in MicroCT rooms at all times.

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• Gloves are provided. Users should bring their own safety glasses/ goggles and lab coat if needed. Shared use of lab coats are not recommended.

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• Gloves should be used on keyboard and mouse.

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• NEVER spray any liquids into the workstation, tape, tape drive, and scanner. They are not water resistant!

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Setup a Scan: Emergency Stop Button

In case of emergency, you can push the Emergency Stop Button.

Pushing this button will immediately stop the power of µCT scanner.

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µCT 35

µCT 45

Setup a Scan: Emergency Stop Button

In case of emergency, you can push the Emergency Stop Button.

Pushing this button will immediately stop the power of µCT scanner.

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VivaCT 80

Setup a Scan: Basic Steps

1. Wrap & put the sample into the sample holder.
2. Place the sample holder onto the rotation stage inside the scanner.
3. Create sample folder (setup sample name)
4. Perform a scout view (preview)
5. Select the region of interests
6. Submit the scan jobs.

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Video Tutorials of scan setup can be found:

https://www.med.upenn.edu/orl/uct/user-tutorials.html

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Setup a Scan: Sample Holders

• The smaller diameter of sample holder, the higher (better) scan resolution can be achieved.
• Sample holders on µCT 35: �(holder diameter) 7mm, 11.5mm, 20mm, 30mm, 37mm
• Sample holders on µCT 45: �(holder diameter) 9mm, 14mm, 24mm, 34mm, 48mm
• If unsure to use which holder, please consult with the manager.

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Sample holders on µCT 35

Sample holders on µCT 45

Setup a Scan: Sample Holders

• Due to limited sample holders, users are responsible for removing their samples from the sample holder after the scan is finished.

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Common Q&A:

Q: All sample holders are full of samples. I am unable to find any empty sample holder to load my scan. What should I do?

�A: You may relocate those samples into a centrifuge tube. You have priority to use the sample holder at your reserved time slot. It is always the users’ responsibility to retrieve samples after scans conclude.

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Setup a Scan: Sample Holders

• Depending on your scan resolution, you may prepare your sample in 15 or 50 mL centrifuge tube, and place the centrifuge tube into the sample holder.
• Make sure you push the 15 or 50 mL centrifuge tube into the bottom of the sample holder.
• No space should be allowed between the centrifuge tube and the sample holder bottom.
• Excessive height above the sample holder can cause accidents!

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Example of 50 mL centrifuge tube in a sample holder

Setup a Scan: Put Sample into Sample Holder

This video (from 0:00 to 6:50) shows how to wrap & put the sample into the sample holder.

https://www.youtube.com/watch?v=QUt0QqIYJ80

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• The liquid you can fill in the sample holder includes PBS, ethanol, water, 10% formalin, or any other non-radiographic medium, depending on the post-processing of your sample.
• Make sure your samples are securely tight (inside the gauze) in the sample holder. �This is IMPORTANT to avoid motion artifacts during scanning.

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Setup a Scan: Put Sample into Sample Holder

This video (from 0:00 to 6:50) shows how to wrap & put the sample into the sample holder.

https://www.youtube.com/watch?v=QUt0QqIYJ80

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• Use parafilm or holder cap to COMPLETELY seal the top of the sample holder.�IMPORTANT to avoid liquid leakage from the sample holder, which can damage the scanner!!!
• Make sure every part of the parafilm is tightly attached to the holder. Trim extra parafilm accordingly.

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Setup a Scan: Put Sample into Sample Holder

This video (from 0:00 to 6:50) shows how to wrap & put the sample into the sample holder.

https://www.youtube.com/watch?v=QUt0QqIYJ80

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Before loading the sample holder into the scanner:

Make sure to use paper towel to wipe any liquid outside the sample holder, which can damage the scanner!!!

Setup a Scan: the Control Box

• The control box is located at the left bottom of the screen.

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Setup a Scan: Run into an Error?

• It’s common for users to run into errors when operating the scanner.

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• Please use cellphone to capture photos of the error message, and send to the manager.

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• If the manager is not available at the time, you may check the �MicroCT Troubleshooting Guide�https://www.med.upenn.edu/orl/uct/assets/user-content/documents/microct-troubleshooting-guide.pdf

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Setup a Scan: Opening the Door

• Before opening the door, please confirm there is NO ongoing scan:�Type “que” in the command window, and press Enter to confirm there is NO “MEASUREMENT” showing up.

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Example of No ongoing scan

Open the door

Setup a Scan: Create Sample Folder

• Click the first left button in the Control box to create sample folder
• Sample name should follow this format:�PI’s initial_your name or Pennkey_Sample info�E.g.: XSL_yilu_1year_F3321

Note: PI’s initial should comes first (for billing purpose).

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Setup a Scan: Perform a Scout View

• Click the second left button in the Control box to open scan software.

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Setup a Scan: Select the ROI

• Once the scout view is finished, select the Region Of Interests (ROI):
• Zooming in/out: Click and hold the mouse Middle button
• Moving: Click and hold the mouse Right button
• Adjusting contrast: �Click and hold both the mouse Middle button and Shift key

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Setup a Scan: Estimate Scan Time

• Once your scan region is selected, the estimated time will be shown on the scan software. The actual time is longer than that, usually at a factor of 1.4. �E.g.: In the scout view shown below, the estimated time is 41.0 min, the actual scan time will be approximately 57 (= 41 x 1.4) min.

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Setup a Scan: Submit Scan Jobs

• Before submit scan jobs, please double check if all info in the “Tasks” window are correct.
• S = Sample number, P = Position
• C = Controlfile, # = Slice number

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Setup a Scan: Scan Schedule

• Please be considerate of other users’ reservations.

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• Any scan extending 10 min into other user’s period will be stopped by manager.

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Common Q&A:

Q: I already reserved 1:00pm to start a scan, but the last user’s scan hasn’t finished. What should I do?

�A: Only 10 min grace period is allowed. If the scan is not finished by 1:10pm, please contact the manager to stop the scan.

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After a Scan: Sample Removal

• Users are responsible for removing their samples from the sample holder after the scan is finished.
• Users may leave notes & contact info to inform the following user on what to do with their sample in the holder.
• If users are unable to locate an empty sample holder and did not receive any instructions from the previous user, they may relocate the samples into a centrifuge tube.
• We will discard any unattended samples two weeks after scanning.

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• After a scan, users should:
• Clean up the bench
• NOT turn off the µCT scanner
• NOT “session out” (log out) the system

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After a Scan: µCT Analysis

• Analysis computes are located in office 315
• Users should sign up on the calendars for using the analysis computers.

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After a Scan: µCT Analysis

• Please view our tutorials and instructions on:�https://www.med.upenn.edu/orl/uct/user-tutorials.html

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After a Scan: Data Storage Policy

• Due to limited disk space, µCT image files will be removed from servers to offline tapes within 3 months after scanning.

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• We suggest users finish µCT analysis within 3 months after scanning.

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• Retrieving image files from tapes is very time consuming and depends on the availability of both tape drive and server space. �Please send tape file retrieval request at least 7 days in advance!�Note: Tape Retrieval Request Form can be downloaded here�https://www.med.upenn.edu/orl/uct/user-tutorials.html

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Rates and Billing

Training rate:

• $100 fee for the first user of the new lab, and $50 fee for the other users within the same lab.

Equipment rate (Self-Service):

• $25/hour. (This fee is subject to change depending on equipment usage and maintenance.)

Image Analysis rate (Self-service):

• Free

Image Importing rate (Full-service):

• $10/sample

Full-Service rate:

• $50/hour for scan. $50/hour for analysis.

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Rates and Billing

• Scans are charged based on the X-ray running time.
• Test/Trial scans for pilot studies operated by the manager are free of charge.
• Problematic scans due to equipment malfunctions will not be charged/billed. Otherwise scans are not refundable.
• Quarterly invoices and detailed usage records are sent to PIs at the end of each billing cycle.

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Funding & Your Future Publications

The MicroCT Imaging Core is supported by Penn Center for Musculoskeletal Disorders (NIH/NIAMS P30 AR069619)

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• If you use data obtained in our MicroCT Core, please include “Penn Center for Musculoskeletal Disorders (P30-AR069619)” in the acknowledgment of the publication.

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Resources

• User tutorials https://www.med.upenn.edu/orl/uct/user-tutorials.html
• MicroCT Troubleshooting Guide�https://www.med.upenn.edu/orl/uct/assets/user-content/documents/microct-troubleshooting-guide.pdf
• We strongly recommend users read the following paper before starting a µCT project.

Bouxsein, Mary L., et al. "Guidelines for assessment of bone microstructure in rodents using micro–computed tomography." Journal of bone and mineral research 25.7 (2010): 1468-1486.�https://asbmr.onlinelibrary.wiley.com/doi/full/10.1002/jbmr.141

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Thank you!

Please let us know if you have any suggestions or comments on this online training!

pcmd.microct@gmail.com

Penn Center for Musculoskeletal Disorders