Using Scipion for stream image processing at Cryo-EM facilities

doi:10.1016/j.jsb.2018.10.001

. 2018 Dec;204(3):457-463.

doi: 10.1016/j.jsb.2018.10.001. Epub 2018 Oct 5.

Using Scipion for stream image processing at Cryo-EM facilities

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.

PMID: 30296492
PMCID: PMC6303188
DOI: 10.1016/j.jsb.2018.10.001

Using Scipion for stream image processing at Cryo-EM facilities

J Gómez-Blanco et al. J Struct Biol. 2018 Dec.

. 2018 Dec;204(3):457-463.

doi: 10.1016/j.jsb.2018.10.001. Epub 2018 Oct 5.

Authors

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.

PMID: 30296492
PMCID: PMC6303188
DOI: 10.1016/j.jsb.2018.10.001

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.

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Figures

**Fig. 1**
Graphical representation of the data flow through the CNB facility. Green, blue and red lines represent the microscope private network, the CNB local area network and the public (WAN) networks respectively.

**Fig. 2**
Overview of the Session Wizard developed at SciLifeLab. (A) The user triggers the wizard for any of the current microscopes. (B) The wizard retrieves project information from the *Application Portal* and reservation details from the *Booking System*. (C) The wizard creates data folders, executes the image copying script, configures the Scipion streaming project and logs the current session into a database. (D) The *Scipion* project is used to generate on the fly web reports and invoice documents later on.

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References

1. Abrishami V., Vargas J., Li X., Cheng Y., Marabini R., Sorzano C.O., Carazo J.M. Alignment of direct detection device micrographs using a robust Optical Flow approach. J. Struct. Biol. 2015;189(3):163–176. - PubMed
1. Biyani N., Righetto R.D., McLeod R., Caujolle-Bert D., Castano-Diez D., Goldie K.N., Stahlberg H. Focus: the interface between data collection and data processing in cryo-EM. J. Struct. Biol. 2017;198(2):124–133. - PubMed
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1. de la Rosa-Trevín J., Quintana A., del Cano L., Zaldívar A., Foche I., Gutiérrez J., Gómez-Blanco J., Burguet-Castell J., Cuenca-Alba J., Abrishami V., Vargas J., Otón J., Sharov G., Vilas J., Navas J., Conesa P., Kazemi M., Marabini R., Sorzano C., Carazo J. Scipion: a software framework toward integration, reproducibility and validation in 3d electron microscopy. J. Struct. Biol. 2016;195(1):93–99. - PubMed
1. Delageniere S., Brenchereau P., Launer L., Ashton A.W., Leal R., Veyrier S., Gabadinho J., Gordon E.J., Jones S.D., Levik K.E., McSweeney S.M., Monaco S., Nanao M., Spruce D., Svensson O., Walsh M.A., Leonard G.A. ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics. 2011;27(22):3186–3192. - PubMed

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[1] Abrishami V., Vargas J., Li X., Cheng Y., Marabini R., Sorzano C.O., Carazo J.M. Alignment of direct detection device micrographs using a robust Optical Flow approach. J. Struct. Biol. 2015;189(3):163–176. - PubMed

[2] Abrishami V., Vargas J., Li X., Cheng Y., Marabini R., Sorzano C.O., Carazo J.M. Alignment of direct detection device micrographs using a robust Optical Flow approach. J. Struct. Biol. 2015;189(3):163–176. - PubMed

[3] Biyani N., Righetto R.D., McLeod R., Caujolle-Bert D., Castano-Diez D., Goldie K.N., Stahlberg H. Focus: the interface between data collection and data processing in cryo-EM. J. Struct. Biol. 2017;198(2):124–133. - PubMed

[4] Biyani N., Righetto R.D., McLeod R., Caujolle-Bert D., Castano-Diez D., Goldie K.N., Stahlberg H. Focus: the interface between data collection and data processing in cryo-EM. J. Struct. Biol. 2017;198(2):124–133. - PubMed

[5] Clare D.K., Siebert C.A., Hecksel C., Hagen C., Mordhorst V., Grange M., Ashton A.W., Walsh M.A., Grunewald K., Saibil H.R., Stuart D.I., Zhang P. Electron Bio-Imaging Centre (eBIC): the UK national research facility for biological electron microscopy. Acta Crystallogr D Struct. Biol. 2017;73(Pt 6):488–495. - PMC - PubMed

[6] Clare D.K., Siebert C.A., Hecksel C., Hagen C., Mordhorst V., Grange M., Ashton A.W., Walsh M.A., Grunewald K., Saibil H.R., Stuart D.I., Zhang P. Electron Bio-Imaging Centre (eBIC): the UK national research facility for biological electron microscopy. Acta Crystallogr D Struct. Biol. 2017;73(Pt 6):488–495. - PMC - PubMed

[7] de la Rosa-Trevín J., Quintana A., del Cano L., Zaldívar A., Foche I., Gutiérrez J., Gómez-Blanco J., Burguet-Castell J., Cuenca-Alba J., Abrishami V., Vargas J., Otón J., Sharov G., Vilas J., Navas J., Conesa P., Kazemi M., Marabini R., Sorzano C., Carazo J. Scipion: a software framework toward integration, reproducibility and validation in 3d electron microscopy. J. Struct. Biol. 2016;195(1):93–99. - PubMed

[8] de la Rosa-Trevín J., Quintana A., del Cano L., Zaldívar A., Foche I., Gutiérrez J., Gómez-Blanco J., Burguet-Castell J., Cuenca-Alba J., Abrishami V., Vargas J., Otón J., Sharov G., Vilas J., Navas J., Conesa P., Kazemi M., Marabini R., Sorzano C., Carazo J. Scipion: a software framework toward integration, reproducibility and validation in 3d electron microscopy. J. Struct. Biol. 2016;195(1):93–99. - PubMed

[9] Delageniere S., Brenchereau P., Launer L., Ashton A.W., Leal R., Veyrier S., Gabadinho J., Gordon E.J., Jones S.D., Levik K.E., McSweeney S.M., Monaco S., Nanao M., Spruce D., Svensson O., Walsh M.A., Leonard G.A. ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics. 2011;27(22):3186–3192. - PubMed

[10] Delageniere S., Brenchereau P., Launer L., Ashton A.W., Leal R., Veyrier S., Gabadinho J., Gordon E.J., Jones S.D., Levik K.E., McSweeney S.M., Monaco S., Nanao M., Spruce D., Svensson O., Walsh M.A., Leonard G.A. ISPyB: an information management system for synchrotron macromolecular crystallography. Bioinformatics. 2011;27(22):3186–3192. - PubMed

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Using Scipion for stream image processing at Cryo-EM facilities

Affiliations

Using Scipion for stream image processing at Cryo-EM facilities

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Affiliations

Abstract

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