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

The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimen must be tightly coupled to data pre-processing to ensure best data quality and microscope usage. Here we provide Warp, a software for real-time evaluation and pre-processing of cryo-EM data during their acquisition. Warp corrects micrographs for global and local motion, estimates the local defocus with the use of novel algorithms, 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 from 3.9 Å to 3.2 Å through fully automated processing of a published cryo-EM data set for influenza virus hemagglutinin. Warp is easy to install, computationally inexpensive, and has an intuitive and streamlined user interface.