TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 33177513.
- Also identified by DOI 10.1038/s41467-020-19513-2 and PMC identifier 7658977.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.