Thomas Fish


Thomas Fish is a Research Software Engineer focused on beamline automation for B24. Thomas joined Diamond in 2019.

Tel: +44 (0)1235 778042

Thomas Fish is a Research Software Engineer who has been working at Diamond since April 2019. His work focuses on developing and maintaining software for the automation of beamline B24.

Since joining Diamond, he has worked closely with the staff and users of B24. Thomas is an integrated member of the B24 team, enabling him to have a more in-depth understanding of the workflow and specific requirements at B24 than would have otherwise been possible. As part of the beamline, Thomas has been responsive to feedback and used his understanding of B24 to better target the needs of staff and users, often suggesting and implementing novel improvements.

Thomas has developed various tools for the beamline and its users, including:

  • txrm2tiff: an open-source Python package to easily inspect and convert xrm & txrm files from our SXT microscope.
  • StitchM: an open-source Python package to stitch the mosaic output from Cockpit (cryoSIM control software), including region of interest markers.
  • GridSNAP: a Python-based graphical application for semi-automatic alignment of the brightfield mosaics (grid mapping) between two microscopes such that regions of interest from one can more efficiently be imaged on the other.
  • XMBatch: automated X-ray data acquisition software. XMBatch enables users to use their beamtime more efficiently by making it possible (and easy) to set up large batches of scans and safely run them unattended.

In addition to the above, Thomas helps at the beamline by supporting staff and users with computer/software issues (working as an intermediary to Scientific Computing as needed), ensuring software is available and up to date on B24's processing PCs, and supporting the move to provide remote beamline access.

Nina Vyas, Stephan Kunne, Thomas M. Fish, Ian M. Dobbie, Maria Harkiolaki, Perrine Paul-Gilloteaux (2021). Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images. STAR Protocols, 2, 2. doi:10.1016/j.xpro.2021.100529

Vyas, N., Perry, N., Okolo, C. A., Kounatidis, I., Fish, T. M., Nahas, K. L., Jadhav, A., Koronfel, M. A., Groen, J., Pereiro, E., Dobbie, I. M., Harkiolaki, M. (2021). Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells. JoVE (171), e62274, doi:10.3791/62274

Kounatidis, Ilias, Stanifer, Megan L., Phillips, Michael A., Paul-Gilloteaux, Perrine, Heiligenstein, Xavier, Wang, Hongchang, Okolo, Chidinma A., Fish, Thomas M., Spink, Matthew C., Stuart, David I., Davis, Ilan, Boulant, Steeve, Grimes, Jonathan M., Dobbie, Ian M., Harkiolaki, Maria (2020). 3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway. Cell, 182, doi:10.1016/j.cell.2020.05.051

Sheardown, Alex, Fish, Thomas M., Roediger, Elke, Hunt, Matthew, ZuHone, John, Su, Yuanyuan, Kraft, Ralph P., Nulsen, Paul, Churazov, Eugene, Forman, William, Jones, Christine, Lyskova, Natalya, Eckert, Dominique, De Grandi, Sabrina. A New Class of X-Ray Tails of Early-type Galaxies and Subclusters in Galaxy Clusters: Slingshot Tails versus Ram Pressure Stripped Tails (2019). The Astrophysical Journal, 112, doi:10.3847/1538-4357/ab0c06

Su, Yuanyuan, Kraft, Ralph, Fish, Thomas Marrick, Sheardown, Alex, Roediger, Elke, Nulsen, Paul, ZuHone, John, Churazov, Eugene, Forman, William, Jones, Christine, Irwin, J, Randall, Scott (2019). Bulletin of the American Astronomical Society, 51, 476

Sheardown, Alex, Roediger, Elke, Su, Yuanyuan, Kraft, Ralph P., Fish, Thomas, ZuHone, John A., Forman, William R., Jones, Christine, Churazov, Eugene, Nulsen, Paul E. J. (2018). The Astrophysical Journal, 865, 118, doi:10.3847/1538-4357/aadc0f


  • MSc Physics (Research), University of Hull
  • BSc (Hons) Physics with Astrophysics, University of Hull

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