Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Autor:	Conesa P; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Fonseca YC; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Jiménez de la Morena J; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Sharov G; Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom., de la Rosa-Trevín JM; St. Jude Children's Research Hospital, Memphis, TN, USA., Cuervo A; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., García Mena A; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Rodríguez de Francisco B; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Del Hoyo D; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Herreros D; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Marchan D; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Strelak D; National Center of Biotechnology (CNB-CSIC), Madrid, Spain.; Masaryk University, Brno, Czech Republic., Fernández-Giménez E; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Ramírez-Aportela E; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., de Isidro-Gómez FP; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Sánchez I; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Krieger J; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Vilas JL; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Del Cano L; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Gragera M; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Iceta M; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Martínez M; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Losana P; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Melero R; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Marabini R; National Center of Biotechnology (CNB-CSIC), Madrid, Spain.; Superior Polytechnic School, Autonomous University of Madrid, Madrid, Spain., Carazo JM; National Center of Biotechnology (CNB-CSIC), Madrid, Spain., Sorzano COS; National Center of Biotechnology (CNB-CSIC), Madrid, Spain.
Jazyk:	angličtina
Zdroj:	Biological imaging [Biol Imaging] 2023 Jun 29; Vol. 3, pp. e13. Date of Electronic Publication: 2023 Jun 29 (Print Publication: 2023).
DOI:	10.1017/S2633903X23000132
Abstrakt:	Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing. Competing Interests: The authors declare no competing interests exist. (© The Author(s) 2023.)
Databáze:	MEDLINE
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