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| Item Type: | Article |
|---|---|
| Title: | An automated workflow for parallel processing of large multiview SPIM recordings |
| Creators Name: | Schmied, C., Steinbach, P., Pietzsch, T., Preibisch, S. and Tomancak, P. |
| Abstract: | Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here we introduce an automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. |
| Keywords: | Computing Methodologies, Microscopy, Programming Languages, Software, Workflow |
| Source: | Bioinformatics |
| ISSN: | 1367-4803 |
| Publisher: | Oxford University Press |
| Volume: | 32 |
| Number: | 7 |
| Page Range: | 1112-1114 |
| Date: | 1 April 2016 |
| Additional Information: | Availability: The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT. The source code can be downloaded from github: https://github.com/mpicbgscicomp/snakemake-work-flows. Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multi-view_Reconstruction. Contact: schmied@mpi-cbg.de |
| Official Publication: | https://doi.org/10.1093/bioinformatics/btv706 |
| PubMed: | View item in PubMed |
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