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

Markus Stabrin, Fabian Schoenfeld, Thorsten Wagner, Sabrina Pospich, Christos Gatsogiannis and Stefan Raunser ()
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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

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19513-2

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