Using Scipion for stream image processing at Cryo-EM facilities

J Gómez-Blanco; J M de la Rosa-Trevín; R Marabini; L Del Cano; A Jiménez; M Martínez; R Melero; T Majtner; D Maluenda; J Mota; Y Rancel; E Ramírez-Aportela; J L Vilas; M Carroni; S Fleischmann; E Lindahl; A W Ashton; M Basham; D K Clare; K Savage; C A Siebert; G G Sharov; C O S Sorzano; P Conesa; J M Carazo

doi:10.1016/j.jsb.2018.10.001

Using Scipion for stream image processing at Cryo-EM facilities

J Struct Biol. 2018 Dec;204(3):457-463. doi: 10.1016/j.jsb.2018.10.001. Epub 2018 Oct 5.

Authors

J Gómez-Blanco¹, J M de la Rosa-Trevín², R Marabini³, L Del Cano⁴, A Jiménez⁴, M Martínez⁴, R Melero⁴, T Majtner⁴, D Maluenda⁴, J Mota⁴, Y Rancel⁴, E Ramírez-Aportela⁴, J L Vilas⁴, M Carroni², S Fleischmann², E Lindahl⁵, A W Ashton⁶, M Basham⁶, D K Clare⁶, K Savage⁶, C A Siebert⁶, G G Sharov⁷, C O S Sorzano⁴, P Conesa⁴, J M Carazo⁴

Affiliations

¹ Department of Anatomy and Cell Biology, McGill University, Montreal, Canada.
² Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
³ Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain. Electronic address: roberto.marabini@uam.es.
⁴ Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain.
⁵ Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden.
⁶ Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom.
⁷ Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, United Kingdom.

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.

Keywords: Electron microscopy; High throughput; Image processing; Live processing; Scipion; Streaming.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computational Biology / methods
Cryoelectron Microscopy / methods*
Image Processing, Computer-Assisted / methods*
Imaging, Three-Dimensional / methods*
Reproducibility of Results
Software*

Abstract

Publication types

MeSH terms

Grants and funding