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SciJava Interface for Parallel Execution in the ImageJ Ecosystem

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Computer Information Systems and Industrial Management (CISIM 2018)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11127))

Abstract

ImageJ has become a popular software platform for image processing and its community has developed and made available numerous plugins for scientific audiences. Nevertheless, no platform-wide solution for parallel processing of big data has been created so far. As ImageJ is a part of the SciJava collaboration project, we propose the concept of seamlessly integrating parallelization-providing capability into one of the SciJava libraries. Specifically, this approach strives to make high-performance infrastructure accessible to ImageJ plugin developers whilst remaining extensible and technology-agnostic. Two parallelization approaches were created and experimentally evaluated on an HPC infrastructure. The results indicate good scalability and are promising for prospective integration of the created functionality into the SciJava Common library.

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Notes

  1. 1.

    https://github.com/imagej/imagej-server/wiki/Rationale.

  2. 2.

    https://github.com/imagej/imagej-server.

  3. 3.

    https://docs.it4i.cz/salomon/hardware-overview/.

  4. 4.

    Super-resolution microscopy frame, available at https://idr.openmicroscopy.org, ID 3138072.

  5. 5.

    https://github.com/PetrBainar/scijava-parallel.

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Acknowledgement

This work was supported by the European Regional Development Fund in the IT4Innovations national supercomputing center – path to exascale project, project number CZ.02.1.01/0.0/0.0/16_013/0001791 within the Operational Programme Research, Development and Education.

We would like to thank Curtis Rueden from Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison for his assistance and comments that greatly improved this work.

Author information

Authors and Affiliations

  1. Department of Computer Science, FEECS, VŠB – Technical University of Ostrava, 17. listopadu 15, 708 33, Ostrava, Poruba, Czech Republic

    Michal Krumnikl, Jan Kožusznik & Pavel Moravec

  2. IT4Innovations, VŠB – Technical University of Ostrava, 17. listopadu 15, 708 33, Ostrava, Poruba, Czech Republic

    Michal Krumnikl, Petr Bainar, Jana Klímová, Jan Kožusznik, Pavel Moravec, Václav Svatoň & Pavel Tomančák

  3. Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany

    Pavel Tomančák

Authors
  1. Michal Krumnikl
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  2. Petr Bainar
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  3. Jana Klímová
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  4. Jan Kožusznik
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  5. Pavel Moravec
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  6. Václav Svatoň
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  7. Pavel Tomančák
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Corresponding author

Correspondence to Michal Krumnikl .

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Editors and Affiliations

  1. Bialystok University of Technology, Bialystok, Poland

    Khalid Saeed

  2. Warsaw University of Technology, Warsaw, Poland

    Władysław Homenda

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Krumnikl, M. et al. (2018). SciJava Interface for Parallel Execution in the ImageJ Ecosystem. In: Saeed, K., Homenda, W. (eds) Computer Information Systems and Industrial Management. CISIM 2018. Lecture Notes in Computer Science(), vol 11127. Springer, Cham. https://doi.org/10.1007/978-3-319-99954-8_25

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  • DOI: https://doi.org/10.1007/978-3-319-99954-8_25

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  • Online ISBN: 978-3-319-99954-8

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