After Beamtime


Copying Data

Data generated at BMIT is quite large and transfer of files will take time. Ideally data transfer should be performed during your beamtime. At no point after your beamtime connecting a hard drive to computers in control room is allowed. If you need to copy your files after your beamtime ask your primary point of contact.

Data Storage

BMIT User Data Back-up Policy

BMIT currently backs up users' data to WestGrid servers (part of Compute Canada). Disk storage space on WestGrid servers is provided based on a competitive review process, meaning that we do not have direct control on the availability of this resource. BMIT's data retention policy at the present time is 1 year - we will strive to keep a back-up copy of all users' data for a period of 2 years, but we cannot guarantee that. At the end of this retention period, data will be evaluated for its ongoing value and relevance. If data is deemed no longer necessary, it will be securely disposed of following data sanitization procedures. Please note that at no point we back-up the reconstructed and processed data, and that is the sole responsibility of the research groups. Files created by users during data analysis and reconstruction (i.e. "rec" folders) will automatically be deleted 90 days after they are generated.

Typical Data Size

The size of collected data at BMIT varies based on the pixel size of the detector, number of projections, number of samples, speed of imaging, etc.; hence ranges from tens of MB for projection imaging to tens of GB for a micro-CT dataset. For a typical experiment on BMIT collecting raw data of 500GB per day is normal. The reconstruction typically generates 2 to 4 times more data depending on the bitdepth of the outcome slices. 

Data Transfer

We ask our users to be prepared for copying the volume of data they will generate at BMIT. Having 2-3 TB of free space is advised. Data transfer can be done by means of bringing an external hard drive, or via network transfer. We recommend copying data to a hard drive as soon as you collect the dataset. Network data transfer needs to be setup after the experiment and can be slower than local transfer depending on your home institution internet speed and other factors. The CLS has setup a new server using Globus to better link users to projects that they are affiliated with and can now access their data directly online, eliminating the need to perform mass copying of projects when users need to retrieve their data. Users can find a personal download for Globus at https://www.globus.org/globus-connect-personal, and once setup, will receive an email from the Globus server to access their data.

Shipping

If you need to ship samples or equipment back to your institution, please consult CLS Shipping webpage.

End of Experiment Feedback

Several days after your beamtime, you will receive an email from the CLS User Office to complete a User Experience Survey. We would greatly appreciate any feedback based on your experience that will help us to improve our services to you and future users.

Data Analysis

Data processing including data reconstruction, stitching of slices for large samples, and data visualization can be performed in BMIT computer lab during or after beamtime. User should ask the primary point of contact to book the computer for s/he. At any point the priority for using BMIT computation infrastructure is with a research team that is collecting data at that time. Users can use BMIT data processing software at BMIT or other software of their choosing at their home institution.

Acknowledging the CLS

Researchers are asked to acknowledge the beamline(s), as well as the participation of any beamline staff who may have assisted in any aspect of an experiment, and include the following statement when presenting results from the CLS:

Part or all of the research described in this paper was performed at the Canadian Light Source, a national research facility of the University of Saskatchewan, which is supported by the Canada Foundation for Innovation (CFI), the Natural Sciences and Engineering Research Council (NSERC), the National Research Council (NRC), the Canadian Institutes of Health Research (CIHR), the Government of Saskatchewan, and the University of Saskatchewan.

  • To refer to technical specifications of BMIT beamlines, they please cite:

Gasilov, Sergey; Webb, M. Adam; Panahifar, Arash; Zhu, Ning; Marinos, Omar; Bond, Toby; Cooper, David M. L.; and Chapman, Dean. (2024) Hard X-ray imaging and tomography at the Biomedical Imaging and Therapy beamlines of Canadian Light Source. Journal of Synchrotron Radiation, 31(5), 1346-1357.

  • To cite the UFO-KIT reconstruction software you may cite:

Faragó, Tomáš; Gasilov, Sergey; Emslie, Iain; Zuber, Marcus; Helfen, Lukas; Vogelgesang, Matthias; Baumbach, Tilo. (2022) Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography. Journal of Synchrotron Radiation, 29(3), 916-927.

Reporting Publications

Researchers are asked to report any publications based on work they performed, in whole or in part, at the Canadian Light Source. The list of the publications reported to the CLS is in important factor in our funding and is taken into account during peer review of research proposals.

Access the list of publications (https://user-portal.lightsource.ca/publications/​), click on the [ + ] button in the top right-hand corner of the page and follow the instructions to provide the requested information in the resulting dialog window. You must be a CLS user to submit a publication.