User Guide –
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.
If you need to ship samples or equipment back to your institution, please consult CLS Shipping webpage.
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 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.
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.
Moreover, if users would like to refer to technical specifications of BMIT beamlines, they may cite the following articles:
- To refer to technical specifications of the BMIT-BM beamline (i.e., 05B1-1 POE-2 endstation):
Wysokinski, T. Chapman, D. Adams, G., Renier, M. Suortti, P. Thomlinson, W. (2007). Beamlines of the biomedical imaging and therapy facility at the Canadian Light Source-Part 1. Nuclear Instruments and Methods in Physics Research A, 582 (1),73-76.
- To refer to technical specifications of the BMIT-ID beamline (i.e., 05ID-2 SOE-1 endstation):
Wysokinski, T. Chapman, D. Adams, G., Renier, M. Suortti, P. Thomlinson, W. (2015). Beamlines of the biomedical imaging and therapy facility at the Canadian Light Source-Part 3. Nuclear Instruments and Methods in Physics Research A, 775(1)1-4.
- 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.
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.