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.
Highlights
The future of projects that require high-end microscopes is through centralized microscopy facilities, in which automatically acquired data needs to be monitored by users and facility staff
As we will show in this article, Scipion differs from these solutions in its larger flexibility, both from the point of view of users and facility staff
The best workflow for each case will depend on specific requirements of specimens, microscopes or facilities, we describe the pipeline offered by default at the National Center for Biotechnology (CNB) cryoEM Facility as use case to clarify Scipion capabilities
Summary
The future of projects that require high-end microscopes is through centralized microscopy facilities, in which automatically acquired data needs to be monitored by users and facility staff. With this scenario in mind, we have redesigned Scipion which is a software framework for integrating several 3DEM software packages through a workflow-based approach (de la Rosa-Trevín et al, 2016). In this way, Scipion starts the processing of the movies as they are being acquired with the double aim of checking for possible data collection errors and executing a user-tailored image processing workflow that provides users with an accurate estimation of the acquired data quality. We describe in detail how Scipion is being used in three representative facilities
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