Using Scipion for stream image processing at Cryo-EM facilities

DOI: 10.1016/j.jsb.2018.10.001

Authors: J. Gómez-Blanco (McGill University) , J. M. De La Rosa-Trevín (Stockholm University) , R. Marabini (National Center for Biotechnology (CSIC)) , L. Del Cano (National Center for Biotechnology (CSIC)) , A. Jiménez (National Center for Biotechnology (CSIC)) , M. Martínez (National Center for Biotechnology (CSIC)) , R. Melero (National Center for Biotechnology (CSIC)) , T. Majtner (National Center for Biotechnology (CSIC)) , D. Maluenda (National Center for Biotechnology (CSIC)) , J. Mota (National Center for Biotechnology (CSIC)) , Y. Rancel (National Center for Biotechnology (CSIC)) , E. Ramírez-Aportela (National Center for Biotechnology (CSIC)) , J. I. Vilas (National Center for Biotechnology (CSIC)) , M. Carroni (Stockholm University) , S. Fleischmann (Stockholm University) , E. Lindahl (Stockholm University; KTH Royal Institute of Technology) , A. W. Ashton (Diamond Light Source) , M. Basham (Diamond Light Source) , D. K. Clare (Diamond Light Source) , K. Savage (Diamond Light Source) , C. A. Siebert (Diamond Light Source) , G. G. Sharov (Medical Research Council Laboratory of Molecular Biology) , C. O. S. Sorzano (National Center for Biotechnology (CSIC)) , P. Conesa (National Center for Biotechnology (CSIC)) , J. M. Carazo (National Center for Biotechnology (CSIC))
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Structural Biology

State: Published (Approved)
Published: October 2018

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.

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

Subject Areas: Information and Communication Technology, Biology and Bio-materials

Diamond Offline Facilities: Electron Bio-Imaging Centre (eBIC)
Instruments: Krios I-Titan Krios I at Diamond

Added On: 09/10/2018 14:01

Documents:
1-s2.0-S1047847718302740-main.pdf

Discipline Tags:

Information & Communication Technologies Structural biology Data processing Life Sciences & Biotech

Technical Tags:

Microscopy Electron Microscopy (EM) Cryo Electron Microscopy (Cryo EM)