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TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM

Author

Listed:
  • Markus Stabrin

    (Max Planck Institute of Molecular Physiology)

  • Fabian Schoenfeld

    (Max Planck Institute of Molecular Physiology)

  • Thorsten Wagner

    (Max Planck Institute of Molecular Physiology)

  • Sabrina Pospich

    (Max Planck Institute of Molecular Physiology)

  • Christos Gatsogiannis

    (Max Planck Institute of Molecular Physiology)

  • Stefan Raunser

    (Max Planck Institute of Molecular Physiology)

Abstract

Single particle cryo-EM requires full automation to allow high-throughput structure determination. Although software packages exist where parts of the cryo-EM pipeline are automated, a complete solution that offers reliable on-the-fly processing, resulting in high-resolution structures, does not exist. Here we present TranSPHIRE: A software package for fully-automated processing of cryo-EM datasets 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 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 metrics and microscope settings 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.

Suggested Citation

  • Markus Stabrin & Fabian Schoenfeld & Thorsten Wagner & Sabrina Pospich & Christos Gatsogiannis & Stefan Raunser, 2020. "TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19513-2
    DOI: 10.1038/s41467-020-19513-2
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