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Bioinformatics. 2019 Feb 25. pii: btz140. doi: 10.1093/bioinformatics/btz140. [Epub ahead of print]

SPIM Workflow Manager for HPC.

Author information

Department of Computer Science, FEECS VŠB - Technical University of Ostrava, Ostrava-Poruba, Czech Republic.
IT4Innovations, VŠB - Technical University of Ostrava, Ostrava-Poruba, Czech Republic.
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.



Here we introduce a Fiji plugin utilizing the HPC-as-a-Service concept, significantly mitigating the challenges life scientists face when delegating complex data-intensive processing workflows to HPC clusters. We demonstrate on a common SPIM image processing task that execution of a Fiji workflow on a remote supercomputer leads to improved turnaround time despite the data transfer overhead. The plugin allows the end users to conveniently transfer image data to remote HPC resources, manage pipeline jobs, and visualize processed results directly from the Fiji graphical user interface.


The code is distributed free and open source under the MIT license. Source code:, documentation:


Supplementary data are available at Bioinformatics online.

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