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

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 exi...

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Bibliographic Details
Published in:Nature communications 2020-11, Vol.11 (1), p.5716-5716, Article 5716
Main Authors: Stabrin, Markus, Schoenfeld, Fabian, Wagner, Thorsten, Pospich, Sabrina, Gatsogiannis, Christos, Raunser, Stefan
Format: Article
Language:English
Subjects:
101/28
631/114/1564
631/535/1258/1259
Automation
Clustering
Computer programs
Data acquisition
Data processing
Datasets
Feedback
Feedback loops
Filaments
Humanities and Social Sciences
Learning algorithms
Machine learning
multidisciplinary
Science
Science (multidisciplinary)
Software
Software packages
Workflow
Workstations
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Summary: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. High-throughput single particle cryo-EM, for instance in drug research, requires the automation of the single particle analysis workflow. Here, the authors present TranSPHIRE, a software package that allows the fully-automated, feedback-driven processing of cryo-EM datasets during data acquisition.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-020-19513-2