cisTEM: User-friendly software for single-particle image processing
By Tim Grant, A. Rohou, N. Grigorieff. 2017
727 citations recorded by the source corpus.
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, 200k - 300k 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.
Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Radiation
In Structural Biology
- Dari Kimanius
- Takanori Nakane
- Erik Lindahl
- Frank DiMaio
- Sjors H. W. Scheres
- G. Sharov
- Liyi Dong
- David J. Fleet
In Surfaces, Coatings and Films
- Dari Kimanius
- Erik Lindahl
- Takanori Nakane
- Frank DiMaio
- G. Sharov
- Liyi Dong
- Sjors H. W. Scheres
- Yifan Cheng
Citations in the corpus
- New tools for automated cryo-EM single-particle analysis in RELION-4.0 (2021, methodology): “The cryo-EM resolution revolution [11] further accelerated the focus on user-oriented software developments, with new software packages like SPHIRE [12], cisTEM [13] and the commercial cryoSPARC [14] implementing robust and easy-to-use pipelines for cryo-EM structure determination.”
- Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses (2021, methodology): “559 Particle images were then analysed by 2D classification and initial model reconstruction using SPHIRE 560 [79], cisTEM [80] and Relion 3.”
- Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION (2018, methodology): “, 2007), which have since then been implemented in multiple image processing packages (Sorzano et al., 2004; Scheres, 2012b; Lyumkis et al., 2013; Punjani et al., 2017; Grant et al., 2018).”