Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Abstract

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.

SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time

“…This is escalating the computational demands but opens the possibility of rapid, definitive assessment of samples at the 2D level within the first hour of data collection. Several developers are working to provide solutions for this real-time problem ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 , Tegunov and Cramer, 2019 , Wagner and Raunser, 2020 ). We here describe SIMPLE 3.0, which we have developed to managed data flow in the Central Oxford Structural Molecular Imaging Centre over the last two years.…”

“…SIMPLE 3.0 runs on relatively cheap and scalable CPU resources thus allowing use of existing computer resources to support real-time processing of SP data ( Table 1 , Results below). In contrast to developments that provide data organization tools and interfaces to other software, such as Scipion ( Gomez-Blanco et al, 2018 , Maluenda et al, 2019 ) and Focus ( Biyani et al, 2017 ), our SIMPLE 3.0 suite consists of a collection of novel image processing algorithms that have been tailored and optimized for use in a stream scenario.…”

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

“…In 2019, we published a survey of the analysis of continuous conformational variability of biological macromolecules [60] and reference analysis of the β-galactosidase using streaming in Scipion [61].…”

The evolution of SPHIRE-crYOLO particle picking and its application in automated cryo-EM processing workflows

“…To this end, crYOLO is a crucial part in our software package SPHIRE that we are optimizing to be used in a completely automated fashion 28 . In Scipion, crYOLO is supported for the construction of intelligent workflows 29 . A recent integration of crYOLO into the automatic pipeline of Relion 30 is successfully used at the Electron Bio-Imaging Center (eBIC) at Diamond Light Source 31 .…”