SciJava Ops: an improved algorithms framework for Fiji and beyond.

Autor:	Selzer GJ; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States., Rueden CT; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States., Hiner MC; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States., Evans EL; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States.; Morgridge Institute for Research, Madison, WI, United States., Kolb D; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; KNIME GmbH, Konstanz, Germany., Wiedenmann M; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; KNIME GmbH, Konstanz, Germany., Birkhold C; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; KNIME GmbH, Konstanz, Germany., Buchholz TO; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland., Helfrich S; KNIME GmbH, Konstanz, Germany., Northan B; True North Intelligent Algorithms, Guilderland, NY, United States., Walter A; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States.; Morgridge Institute for Research, Madison, WI, United States.; KNIME GmbH, Konstanz, Germany., Schindelin J; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States.; Morgridge Institute for Research, Madison, WI, United States.; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.; Microsoft Corporation, Redmond, WA, United States., Pietzsch T; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany., Saalfeld S; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, United States., Berthold MR; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany.; KNIME GmbH, Konstanz, Germany., Eliceiri KW; Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, United States.; Morgridge Institute for Research, Madison, WI, United States.
Jazyk:	angličtina
Zdroj:	Frontiers in bioinformatics [Front Bioinform] 2024 Sep 27; Vol. 4, pp. 1435733. Date of Electronic Publication: 2024 Sep 27 (Print Publication: 2024).
DOI:	10.3389/fbinf.2024.1435733
Abstrakt:	Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many "bridge" layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits. The SciJava Ops library presented here addresses this need through two novel principles. Algorithm implementations are declared as plugins called Ops, providing a uniform interface regardless of the toolkit they came from. Users express their needs declaratively to the Op environment, which can then find and adapt available Ops on demand. By using these principles instead of direct function calls, users can write streamlined workflows while avoiding the translation boilerplate of bridge layers. Developers can easily extend SciJava Ops to introduce new libraries and more efficient, specialized algorithm implementations, even immediately benefitting existing workflows. We provide several use cases showing both user and developer benefits, as well as benchmarking data to quantify the negligible impact on overall analysis performance. We have initially deployed SciJava Ops on the Fiji platform, however it would be suitable for integration with additional analysis platforms in the future. Competing Interests: Authors DK, MW, CB, SH, AW, and MB were employed by KNIME GmbH. Author JS was employed by Microsoft Corporation. Author BN was employed by True North Intelligent Algorithms. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision. (Copyright © 2024 Selzer, Rueden, Hiner, Evans, Kolb, Wiedenmann, Birkhold, Buchholz, Helfrich, Northan, Walter, Schindelin, Pietzsch, Saalfeld, Berthold and Eliceiri.)
Databáze:	MEDLINE
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