FAQ About Data from the MCT
FAQ: Data Retrieval
Where is the data stored?
The MCT uploads data to Stanford’s Oak Storage Service (Oak) for retrieval by the user.
How can I access and download the data?
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.
How do I use Globus?
Stanford Libraries has a useful Globus Quick Start guide for new users of Globus.
How long is the data available for download?
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.
Who can access the data?
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.
How can I acknowledge data from the MCT?
Please acknowledge the lab with the following: Stanford University MicroCT Facility (RRID:SCR_025800)
FAQ: Data Archiving
Is the data archived?
Yes, all raw data collected at the MCT is archived to cold cloud storage.
Who can access the archived data?
This data is only accessible to the MCT, but users can request the data should it be needed due to corrupted or lost data.
Does downloading archived data cost anything?
Yes, the provider charges a fee for any archived data pulled out of cold storage. The user is responsible for recouping this cost.
FAQ: Data Interpretation
What is the file format of the data?
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.
What about the rest of the data files in the data folder?
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.
I haven't worked with microCT data before, what software should I use?
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.
The data is too large for my computer, are computing resources available at the MCT?
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.
Is the MCT available for consultation on data processing/analysis?
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.