CryoEM

Many CryoEM software packages part of PReSTO are mentioned in publication from 2021 entitled Using RELION software within the Scipion framework by Dustin Morado, Marta Carroni and José Maria de la Rosa-Trevin from CryoEM SciLifeLab Stockholm and Grigory Sharow from MRC Laboratory of Molecular Biology in Cambridge.

To improve Cryo-EM software documentation in PReSTO, we want support from the Swedish Cryo-EM community! Please email a PReSTO team member and suggest improvements perhaps sharing an example script, links to recent tutorials, or other information helpful to Cryo-EM newcomers.

For instance here is a template script to transfer data from ucem.kbc.umu.se to NSC Berzelius. Exchange USER and PASSWORD, update REMOTE_DIR and LOCAL_DIR, make the script runnable by chmod 755 mirror_lftp_share.sh, and finally run it in the background by ./mirror_lftp_share.sh &.

CCP-EM

CCP-EM stands for Collaborative Computational Project for Electron cryo-Microscopy and aim to support users and developers in biological EM.

cisTEM

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.

crYOLO

crYOLO is an application for fast and accurate cryo-EM particle picking. It’s based on convolutional neural networks and utilizes the popular You Only Look Once (YOLO) object detection system.

CryoSPARC

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy used in research and drug discovery pipelines. Use module avail CryoSPARC to find latest version at NSC Berzelius or Tetralith. A workshop designed to support new users running CryoSPARC on Berzelius was organised by Tim Schulte and Piotr Draczkowski from SciLifeLab in April 2024. Some startup information also at CryoSPARC on Berzelius.

Ctffind

Ctffind finds CTFs of electron micrographs written by Niko Grigorieff and colleagues presented in detail online. Ctffind is available from the PReSTO menu.

EMAN2

EMAN a scientific image processing suite intended for data from transmission electron microscopes. EMAN2 is available from the PReSTO menu.

Gautomatch

Gautomatch is a GPU accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates written by Kai Zhang.

Gctf

Gctf is a GPU accelerated program for accurate estimation of the contrast transfer function (CTF) written by Kai Zhang

MotionCor2

MotionCor2 is multi-GPU accelerated software that corrects for electron beam-induced sample motion presented here and published in 2013

Relion

Relion for REgularised LIkelihood OptimisatioN is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology and published in 2012. Online documentation and gihub repository. Relion-CPU and Relion-GPU is available from the PReSTO menu.

Scipion

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM) published by José Maria de la Rosa-Trevin and colleagues in 2016 and 2021. It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Scipion is available from the PReSTO menu.

Xmipp

Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.