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TranSPHIRE

  • Description

    a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all microscope settings and metrics generated by its individual tools in order to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.

  • Usage

    To list all executables provided by TranSPHIRE, run: $ sbgrid-list transphire Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install transphire Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    M. Stabrin, F. Schoenfeld, T. Wagner, S. Pospich, C. Gatsogiannis, and S. Raunser. 2020. TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM. bioRxiv. 155275.


    • *Full citation information available through

  • Webinars

    TranSPHIRE

    Topic: TranSPHIRE
    Presenter: Markus Stabrin, Max Planck Institute of Molecular Physiology
    TranSPHIRE


    Host: Shaun Rawson
    Recorded on Tuesday, October 27th

  • Keywords

    Electron Microscopy

  • Default Versions

    Linux 64:  1.5.13 (1.1 GB)

  • Other Versions

      Linux 64:

      1.5.11 (1.1 GB) , 1.5.9 (1.2 GB)

  • Developers

    Markus Stabrin

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