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. 2019 Oct 1;35(19):3875-3876.
doi: 10.1093/bioinformatics/btz140.

SPIM workflow manager for HPC

Jan Kožusznik  1   2 , Petr Bainar  2 , Jana Klímová  2 , Michal Krumnikl  1   2 , Pavel Moravec  1   2 , Václav Svatoň  2 , Pavel Tomančák  2   3
Affiliations

SPIM workflow manager for HPC

Jan Kožusznik et al. Bioinformatics. .

Abstract

Summary: 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 Selective Plane Illumination Microscopy 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.

Availability and implementation: The code is distributed free and open source under the MIT license. Source code: https://github.com/fiji-hpc/hpc-workflow-manager/, documentation: https://imagej.net/SPIM_Workflow_Manager_For_HPC.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
An overview of SPIM data processing on an HPC cluster: (a) a screenshot of the SPIM Workflow Manager plugin main window with 11 jobs and a context menu; (b) the dashboard for a selected job processing 10 time points of a SPIM recording; (c) an overview of the proposed solution—left: unregistered and fused SPIM data, middle: the SPIM data processing workflow in Fiji relying on the HEAppE Middleware framework, right: an example of an HPC infrastructure
See this image and copyright information in PMC

References

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