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SciJava Ops : an improved algorithms framework for Fiji and beyond

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Datum

2024

Autor:innen

Selzer, Gabriel J.
Rueden, Curtis T.
Hiner, Mark C.
Evans, Edward L.
Wiedenmann, Marcel
Birkhold, Christian
Eliceiri, Kevin W.
et al.

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Published

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Frontiers in Bioinformatics. Frontiers. 2024, 4, 1435733. eISSN 2673-7647. Verfügbar unter: doi: 10.3389/fbinf.2024.1435733

Zusammenfassung

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.

Zusammenfassung in einer weiteren Sprache

Fachgebiet (DDC)
004 Informatik

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algorithms, image analysis, scientific imaging, imaging software, analysis workflows, Fiji, OpenCV, python

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ISO 690SELZER, Gabriel J., Curtis T. RUEDEN, Mark C. HINER, Edward L. EVANS, David KOLB, Marcel WIEDENMANN, Christian BIRKHOLD, Stefan HELFRICH, Michael R. BERTHOLD, Kevin W. ELICEIRI, 2024. SciJava Ops : an improved algorithms framework for Fiji and beyond. In: Frontiers in Bioinformatics. Frontiers. 2024, 4, 1435733. eISSN 2673-7647. Verfügbar unter: doi: 10.3389/fbinf.2024.1435733
BibTex
@article{Selzer2024-09-27SciJa-71113,
  year={2024},
  doi={10.3389/fbinf.2024.1435733},
  title={SciJava Ops : an improved algorithms framework for Fiji and beyond},
  volume={4},
  journal={Frontiers in Bioinformatics},
  author={Selzer, Gabriel J. and Rueden, Curtis T. and Hiner, Mark C. and Evans, Edward L. and Kolb, David and Wiedenmann, Marcel and Birkhold, Christian and Helfrich, Stefan and Berthold, Michael R. and Eliceiri, Kevin W.},
  note={Article Number: 1435733}
}
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