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.Spanish Ministry of Economy and Competitiveness through Grants BIO2016-76400R(AEI/FEDER, UE) and AEI/FEDER BFU 2016 74868P, the Comunidad Autónoma de Madrid through Grant: S2017/BMD-3817, European Union (EU) and Horizon 2020 through grant Corbel (INFRADEV-1-2014-1, Proposal: 654248). The “Knut & Alice Wallenberg Foundation”, and “A Pilot Facility development grant from Science for Life Laboratory”. European Union (EU) and Horizon 2020 through grant EOSCpilot (INFRADEV-04-2016, Proposal: 739563).This work used the EGI Infrastructure and is co-funded by the EGIEngage project (Horizon 2020) under Grant No. 654142. European Union (EU) and Horizon 2020 through grant West-Life (EINFRA-2015-1, Proposal: 675858) European Union (EU) and Horizon 2020 through grant Elixir - EXCELERATE (INFRADEV-3-2015, Proposal: 676559) European Union (EU) and Horizon 2020 through grant iNEXT (INFRAIA-1-2014-2015, Proposal: 653706).Peer reviewe