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          Institute: MPI für molekulare Zellbiologie und Genetik     Collection: MPI-CBG Publications 2016 (archival)     Display Documents



ID: 732410.0, MPI für molekulare Zellbiologie und Genetik / MPI-CBG Publications 2016 (archival)
An automated workflow for parallel processing of large multiview SPIM recordings.
Authors:Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel
Date of Publication (YYYY-MM-DD):2016
Title of Journal:Bioinformatics (Oxford, England)
Volume:32
Issue / Number:7
Start Page:1112
End Page:1114
Copyright:not available
Audience:Experts Only
Intended Educational Use:No
Abstract / Description: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.
External Publication Status:published
Document Type:Article
Communicated by:Thüm
Affiliations:MPI für molekulare Zellbiologie und Genetik
Identifiers:LOCALID:6382
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