cisTEM, user-friendly software for single-particle image processing

TLDR

cisTEM is an open‑source software designed for high‑resolution cryo‑EM single‑particle data processing. It offers a GUI‑based pipeline that handles movie processing, defocus estimation, automatic particle picking, 2D/3D classification, ab‑initio map generation, high‑resolution refinement, and can be run on workstations or clusters. cisTEM processes typical datasets (≈2000 micrographs, 200–300 k particles) in under half a day on a CPU workstation, comparable to GPU acceleration, and is freely downloadable from cistem.org.

Abstract

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.