Sample submission for CTs
Step 1: Create an account
If you are not currently a BRC user, create an account.
For billing purposes, include your Cornell account number or send in a PO. Scans will not be performed until a payment method is in place.
Step 2: Discuss your experimental needs with the Facility staff
Plan your experiment, read this document, and contact the BRC Imaging staff with your questions. During this discussion, we will assess your needs, discuss your budget, how to prepare your sample, etc.
For example, depending on the structures you want to see, samples may need to be stained. Researchers looking at soft tissue structures or plant cells are generally more satisfied with their results after CT staining.
We will help you make these decisions during the initial project consultation.
Project consultation is also a good time to request a quote, and discuss which format you want your results as prices may vary for raw data, reconstructed, 3D or video format.
Step 3: Send your samples
If you are on campus, you can bring your samples to B46 Weill Hall. Samples brought in person can be left in the black cabinet on the “IN” shelf.
If you need to ship your samples, send them at:
B46 Weill Hall
Here are some general guidelines for sample preparation:
Most samples can be scanned as-is, or with minimal preparation aside from staining. We will sometimes mount a sample with cyanoacrylate glue. Please let us know if this is inappropriate for your sample.
Metals: Metal strongly scatters x-rays, so the smallest diameter that still yields useful information is best (specimens smaller than 1cm in diameter are best)
- Ceramic or polymer materials: Can generally be imaged as-is. Please discuss your needs with the CT staff first.
- Inorganic samples (fossils etc): Can usually be imaged as-is. Soil samples should be in a small plastic container like a conical tube.
- Fabrics/fibers/threads: A few cm of thread or a piece of fabric at least a few mm across is usually best. Please discuss with CT staff prior to your scan if you have any particular imaging requirements (under tension, folded, etc).
- Plant specimens: Samples can be stored in fluid in centrifuge tubes, mounted in paraffin blocks, or imaged as-is. Removing the specimen from the plant is usually preferable but not always necessary.
- Small animal specimens/organs (less than ~1 cm3): We can usually scan these as-is. Imaging through plastic is better than glass; a 15- or 50- mL conical tube is a suitable container. Since a floating sample may move during imaging, we may constrain the sample with a piece of foam prior to scanning.
- Larger animal specimens preserved in alcohol: We will typically remove the animal from its container and place it in a sealed leak-proof bag prior to imaging.
- Bone or shell: Can usually be imaged as-is.
Step 4: Test run
We will help you to figure out whether CT is appropriate for your samples. For preliminary proof-of-principle scans (<1 hr), we will scan your specimen free of charge.
If you want to determine the best parameters for your specimen, we will generally do 2-3 different scans and charge only for whichever parameters are most satisfactory moving forward.
Turnaround time for this scan is usually within 1-2 weeks. Sometimes, we do another iteration if there need to be further changes.
If nothing suits your needs on these preliminary scans, we charge only for the shortest scan.
- If you like the results, we analyze the rest of the samples. Once you have chosen the scan parameters that suits the best your research needs and budget, we use these as a reference to charge the first sample and all the remaining samples.
Step 5: Scanning of samples
After the test run, turnaround time for the rest of the sample depends on the sample queue and how many samples are involved. We can usually guarantee about 10 hours per week on a project with many samples to scan. This means that for single samples, we can typically return data in under a week.
If we can schedule scans in advance, it is usually easier to guarantee a particular timeline. You can inquire about time estimates when you discuss with the staff during the project consultation (step 2).
Step 6: Download the data
We will send you data as they are generated via Cornell Box. We will also send you a final confirmation email once the work has been complete. You will receive data in either a DICOM or TIFF format, where each image is a single slice from the reconstructed CT data. If you want a video or 3D analysis to be performed, please discuss this with the staff beforehand for a price estimate.
For researchers on campus, we can give you access to 3D image processing programs Avizo and Osirix.
Users outside Cornell will need to purchase appropriate imaging and analysis software.Raw data (pre-reconstruction) is held onto for one month before deleting, due to computer space considerations. We hold onto reconstructed CT data for 3 years in backed up, secure servers. If you need old data to be resent or reconstructed again, send us a file name or date when the scan was performed, and we should be able to track it down.