Real-time cryo–EM data pre-processing with Warp

By D. Tegunov, Patrick Cramer. 2018

884 citations recorded by the source corpus.

The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must be tightly coupled to data preprocessing to ensure the best data quality and microscope usage. Here we describe Warp, a software that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Warp corrects micrographs for global and local motion, estimates the local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be fed into established programs for particle classification and 3D-map refinement. Our benchmarks show improvement in the nominal resolution, which went from 3.9 Å to 3.2 Å, of a published cryo-EM data set for influenza virus hemagglutinin. Warp is easy to install from http://github.com/cramerlab/warp and computationally inexpensive, and has an intuitive, streamlined user interface. The user-friendly software tool Warp enables automated, on-the-fly preprocessing of cryo-EM data, including motion correction, defocus estimation, particle picking and image denoising.

Subfields: Molecular Biology, Structural Biology, Surfaces, Coatings and Films, Computational Biology & Bioinformatics

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Citations in the corpus

New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “Recently, the same data were also re-processed in Warp and cryoSPARC, resulting in an improved resolution of 3.2 A˚ ( Tegunov and Cramer, 2018 ).”
Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology (2020, positive): “…S2A4 dataset, 1,995 micrographs were collected with a defocus range comprised between (cid:4) 0.4 and (cid:4) 2.4 m m. Movie frame alignment, estimation of the microscope contrast-transfer function parameters, particle picking and extraction were carried out using Warp (Tegunov and Cramer, 2019).”
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM (2019, methodology): “Besides these programs, Warp 10 and Topaz 11 were recently described in preprints.”
Generation of ordered protein assemblies using rigid three-body fusion (2020, neutral): “…(37 – 41), 3) SAXS sample preparation and analytical tools for data collected at the Structurally Integrated Biology for Life Sciences (SIBYLS) Beamline (42 – 44), 4) negative-stain EM procedures and tools (32, 33, 45, 46), and 5) cryo-EM sample preparation and processing schemes (32, 33, 46 – 57).”