Help Privacy Policy Disclaimer
  Advanced SearchBrowse




Journal Article

SPIM workflow manager for HPC.


Tomančák,  Pavel
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

External Resource
No external resources are shared
Fulltext (restricted access)
There are currently no full texts shared for your IP range.
Fulltext (public)
There are no public fulltexts stored in PuRe
Supplementary Material (public)
There is no public supplementary material available

Kožusznik, J., Bainar, P., Klímová, J., Krumnikl, M., Moravec, P., Svatoň, V., et al. (2019). SPIM workflow manager for HPC. Bioinformatics (Oxford, England), 35(19), 3875-3876. doi:10.1093/bioinformatics/btz140.

Cite as: https://hdl.handle.net/21.11116/0000-0006-7E3A-D
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.