SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time

Joseph Caesar, Cyril F. Reboul, Chiara Machello, Simon Kiesewetter, Molly L. Tang, Justin C. Deme, Steven Johnson, Dominika Elmlund, Susan M. Lea, Hans Elmlund

Research output: Contribution to journalArticleResearchpeer-review

25 Citations (Scopus)


We here introduce the third major release of the SIMPLE (Single-particle IMage Processing Linux Engine) open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA). Development of SIMPLE 3.0 has been focused on real-time data processing using minimal CPU computing resources to allow easy and cost-efficient scaling of processing as data rates escalate. Our stream SPA tool implements the steps of anisotropic motion correction and CTF estimation, rapid template-based particle identification and 2D clustering with automatic class rejection. SIMPLE 3.0 additionally features an easy-to-use web-based graphical user interface (GUI) that can be run on any device (workstation, laptop, tablet or phone) and supports a remote multi-user environment over the network. The new project-based execution model automatically records the executed workflow and represents it as a flow diagram in the GUI. This facilitates meta-data handling and greatly simplifies usage. Using SIMPLE 3.0, it is possible to automatically obtain a clean SP data set amenable to high-resolution 3D reconstruction directly upon completion of the data acquisition, without the need for extensive image processing post collection. Only minimal standard CPU computing resources are required to keep up with a rate of ∼300 Gatan K3 direct electron detector movies per hour. SIMPLE 3.0 is available for download from

Original languageEnglish
Article number100040
Number of pages9
JournalJournal of Structural Biology: X
Publication statusPublished - Jan 2020


  • Cryo-EM
  • Real-time
  • Single-particle
  • Stream image processing

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