Using Scipion for stream image processing at Cryo-EM facilities

Abstract

Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

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

“…Therefore, this abstraction was created to improve the communication between developers through establishing a common language when talking about specific SIMPLE functionalities. This kind of abstraction ought to be helpful also for those developing packages of packages, such as Scipion ( de la Rosa-Trevín et al, 2016 , Gomez-Blanco et al, 2018 ) or Appion ( Lander et al, 2009 ), allowing more rapid integration when new versions of SIMPLE are released. Furthermore, it could provide a framework for integrating other functionalities than SIMPLE within the GUI in the future.…”

“…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.…”

CryoEM structure ofDrosophilaflight muscle thick filaments at 7 Å resolution

“… Resolution was computed using the version of Mono Res embedded within Scipion ( Gomez-Blanco et al, 2018 ). The color bars show the local resolution on each surface in Ångstroms.…”

High-resolution structures of malaria parasite actomyosin and actin filaments

“…The dose per frame was 1.07 e/Å 2 , and we used defoci from 0.8 to 2.6 µm. The movies were aligned with MotionCor2 (42) within the Scipion framework(43). Contrast transfer function was estimated by CTFFind 4.1.5(44), and the resulting 2786 good images were used for further data processing.…”