Fequently Asked Questions About MCT Data

Please acknowledge the lab with the following: Stanford University MicroCT Core Facility (RRID:SCR_025800)

Research Resource Identifiers (RRIDs) are persistent and unique identifiers used to promote discovery and tracking of shared analytical resources.

If you have recent publications (journals, conference abstracts, theses, book chapters, etc.) that includes work performed at the MCT, we would be happy to include a citation of the work on the MCT's publication page. The easiest way to do this is if the MCT was acknowledged with its identifier (RRID:SRC_025800). Otherwise, you can provide the citation directly to us by filling out this Google form.

The MCT uploads data to Stanford’s Oak Storage Service (Oak) for retrieval by the user.

The data can be accessed using Globus. Globus is free for users at non-profit research and education institutions. Oak's Globus endpoint allows the user to access and download the data from a link supplied by the MCT.

Stanford Libraries has a useful Globus Quick Start guide for new users of Globus.

The data is available for at least 30 days before being removed from Oak. Extensions can be made if accepted by the MCT, but the user is solely responsibility to request the extension before the 30-day deadline.

The data is only accessible to the MCT and the user who initiated the scanning request. The user can provide written permission to the MCT to also give access to any collaborators identified by the user.

Yes, if preferred, you may bring an external hard drive to the lab for data transfer.

The file format of the final produced data is a stack of 2D 16-bit TIFF image files. Most image processing software can open this type of image data. If a specific file format such as DICOM is needed, we can try to accommodate those formats on request.

There are also TXT files which include all the metadata like the parameters used to collect the scan and create the reconstructed images. An explanation of all the data files is available for the user.

Most any image processing software can work for microCT data, it is in fact just image data. Many purchasable software are very powerful and sometimes necessary for certain specific applications. But, it is often possible to use free or open-source software or codes for most basic processing and analysis techniques. Some free software to try include Fiji/ImageJ or Dragonfly 3D World, but the software you need can be very dependent on what you need out of your analysis.

In your image processing software of choice, you need to open all of the TIF files in the "recon" or "merge" folder at the same time. The software should read the 2D images as a stack and collate them into one 3D image.

Yes, the MCT has a post-processing workstation available for non-commercial users. Time on the workstation can be requested using the equipment reservation system.

The MCT is designed to be a learning resource for the community. We are happy to consult with you on what resources or techniques could be best suited for your research goals. If needed, the MCT can provide visualizations and processing, especially for collaborative work, but that is at the discretion of the staff.

Yes, all raw data collected at the MCT is archived to cold cloud storage. 

This data is only accessible to the MCT, but users can request the data should it be needed due to corrupted or lost data. 

Yes, the provider charges a fee for any archived data pulled out of cold storage. The user is responsible for recouping this cost.