Full service CT scans: Information and Policies

Scheduling CT scans

Sample submission and information requests should be communicated via the BRC Imaging contact page (select Imaging Facility). Resolution, features of interest, staining methods, budget constraints, and time constraints will need to be discussed to optimize scan protocols.


Sample preparation

Researchers are encouraged to prepare samples as “ready” for scanning as possible. This includes fixing/staining samples as necessary, and mounting samples as necessary.  Fixed samples should not be submitted in formaldehyde, but in 70%-100% ethanol or methanol. Iodine may be used for preferential staining of soft-tissue with high success, although other staining agents exist and may be used as needed. For a reference protocols on staining refer to :

- Comparative staining protocols 

- Iodine staining protocol – rat cardiac tissue

- Iodine staining protocol – mouse cardiac tissue

- Phosphotungstic Acid staining protocol


Dropping off samples

Samples must be left clearly labeled when they are dropped off with the name of the contact person, email address, and sample numbers/names.


Picking up samples

The Imaging facility courteously requests timely collection of samples after being scanned. If research samples are no longer desired, it is the researcher’s responsibility to collect them for proper disposal. The imaging facility reserves the right to dispose of samples not collected after extended periods of time.


Live animal imaging

The Imaging facility does not have an independent IACUC protocol, which requires any lab desiring to do live animal CT to write their own protocol to be approved by the University.  The research lab must provide anesthesia consumables to use with the isoflurane apparatus already in the CT facility.  Researchers are solely responsible for anesthesia dosing and maintenance during the scan. We encourage users to come at least 5-10 minutes early to their appointment time to setup for live animal imaging.


Free scan policy

To encourage use of the CT facility, we are happy to provide one free scan per person/per project as proof of concept/capability of the CT machines. This is to ensure that the machine is capable of producing useful data to the researcher.  The caveat to the free scan is that no data can be used for publication purposes unless the researchers elect to pay for the data.


CT imaging facility rates

Billing for facility time will typically occur at the end of the month that the project is completed. For current funding rates, please refer to the pricing page:  Pricing Page


Facility time is billed in quarter-hour blocks, with the minimum time of 0.5 hours. Facility time encompasses sample preparation & loading, CT scan time, reconstruction of data, and (optionally) any analysis of data.  For users with large-scale projects, volume discount pricing is available.


Transfer of data

Data will be made available in .VFF file format or .DCM file format from the GE CT or in .TIFF format from the Xradia CT. Normally all data will be uploaded to Cornell’s Dropbox server. Since the Dropbox servers will only hold data for a limited time (maximum of 3 weeks), researchers are encouraged to promptly download their data from the server.  For users outside of Cornell, access to the Cornell Dropbox server will be granted on a 6-month temporary white-list.  For users with multiple data sets who are geographically far from Cornell’s server, we can mail a provided hard drive with your data to you.


Data storage

All data, once transferred to the research group, is the responsibility of the research group to catalog and store. Although the facility employs a limited, temporary backup of data on Cornell servers, researchers should not rely on this as an alternative to backing up of their data. If data retrieval is necessary for projects without ongoing CT use, fees will be assessed.


Osirix software

Osirix is free software that runs on Mac computers with an intuitive UI and relatively fast learning curve. For users with large data file sets, we can provide the 64-bit site license upgrade to be installed on their workstation. Because processing CT data is a memory-intensive operation, users are encouraged to use MacPro/iMac workstations with 4-12 CPU cores and 16-32GB RAM, as Macbook Pro laptops usually do not possess the necessary hardware to handle image analysis.   For users who are unable to access Mac workstations, we can arrange scheduling on the facility workstations during off-hours. 



Data analysis

For new users, the CT facility can provide 2D/3D movie visualizations showing slice-through and 3D representations of CT scan data. For more specific analysis, the facility will work with researchers to give them a brief tutorial in Osirix or Microview software so they can begin to analyze their data independently. For complete analysis of data, the CT facility can perform all necessary data analysis in Osirix or VSG Avizo software, billed at the facility rate.