PaleoCT scanner

PaleoCT Scanner Facility

The University of Chicago PaleoCT is a custom-built dual tube X-ray computed tomography (CT) scanner from GE. It is equipped with a 180 kV nano CT tube and a high power 240 kV micro CT tube. This setup allows us to scan very small specimens with a resolution up to 0.4 um using the nano tube or dense fossils using the high power tube.

The PaleoCT scanner is located in Culver Hall, under the direction of the Luo Lab. The PaleoCT lab opened in the summer of 2014 for serving the faculty, students, researchers and staff in the Biological Sciences Division (BSD), as well as users from outside UChicago. PaleoCT is a facility under BSD Office of Shared Research Facilities (OSRF), but the account management and operational support are by Department of Organismal Biology and Anatomy (OBA). Thus the account procedure for using PaleoCT may be different from procedures for other facilities of OSRF.

Each year a small number of students associated with different labs are certified to operate the PaleoCT unit in order to facilitate its use. Outside researchers interested in using the services of the PaleoCT should contact Dr. Luo for an appointment and pricing information.

Who is a good candidate for CT training?

Training sessions for using PaleoCT will be offered when enough UChicago graduate students, postdocs, faculty and staff members have expressed interest. Graduate students, postdocs, or staff members are eligible if they demonstrate the need to use CT as a research tool, and are authorized by their Lab PI’s and/or their supervisors. After the training, trainees will have the responsibility to scan for other researchers in their labs, as directed by the Lab PI’s.

Training will be prioritized for those who plan to use the machine consistently for a longer period of time. Trained users who have not used the scanner in 6 months will be put on the inactive list and their accounts will be re-activated after a review session.

The purpose of limiting the user pool to a smaller number of more active and frequent users is for the safety and good maintenance of the equipment.

We warmly welcome all prospective users to contact us about their need to use our CT scanner as a research tool.

More Information on PaleoCT

Zhe-Xi Luo, Principal Investigator

Ph: (773) 702-7816

E-mail: zxluo@uchicago.edu

 

April Isch Neander, Lab Manager

Ph: (773) 702-4715

E-mail: aisch@uchicago.edu

Girard, Romuald, Hussein A. Zeineddine, Courtney Orsbon, Huan Tan, Thomas Moore, Nick Hobson, Robert Shenkar et al. "Micro-computed tomography in murine models of cerebral cavernous malformations as a paradigm for brain disease." Journal of Neuroscience Methods 271 (2016): 14-24.(doi: 10.1016/j.jneumeth.2016.06.021)

You can make an appointment by contacting April Neander and Dr. Zhe-Xi Luo. Appointments should be made at least two weeks in advance, and at times may need to be made a month in advance.

The default data format is a stack 16 bit TIFF images and all scans come with an informational scan sheet in PDF format. The scan sheet lists scanning parameters as well as information about the specimen and it is highly recommended that you always keep a copy of this file with the scan. We can also provide the data in DICOM format, which is more common among medical scanners. The raw projection files and other associated metadata files can be provided upon request. It is recommended to have the raw data for archiving but these files are also large

Clients from outside the University of Chicago will be emailed an invoice and can pay with check or money order.

The clients will receive their CT data immediately after scanning. A backup copy of the data will be kept as a service and convenience for the client for two years. This service may be subject to change without warning, so it is recommended that you keep backups of your data.

In order to visualize or create a 3D model of your data, we suggest that you use CT software that may be provided by your institution or an open-source version. Some common paid software are Materialise Mimics, VG Studio Max, FEIs Amira and Avizo, ORS Dragonfly, or OsiriX. Some free, open-source CT software include Drishti, 3D Slicer, itk-SNAP, and ImageJ. We do not currently offer a data segmenting service.

The PaleoCT scanner is a GE v|tome|x scanner that can capture any specimen that fits within a 9.5in (24cm) diameter, 9.5in (24cm) high cylinder in a single scan. The scanner has a feature, however, that allows a 15in (38cm) tall object to be captured by taking multiple scans and stitching them together. The machine can physically fit a specimen up to 20in (50.8cm) in height and 14in (35.6cm) diameter, though such a specimen could not be scanned together. It should be noted however, that the resolution (voxel size) of a scan is dependant on the size of the specimen and its mounting structure. The smaller the combined specimen and mount is, the higher the resolution can be. The maximum weight the scanner can allow is 22lbs (10kg).

Internal (UChicago) users: $50/hour

External users: $65/hour