Introduction

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, multichannel, multiillumination 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.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/mpicbg-scicomp/snakemake-workflows Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction: schmied@mpi-cbg.deSupplementary data are available at Bioinformatics online.

Publications

  1. An automated workflow for parallel processing of large multiview SPIM recordings.
    Cite this
    Schmied C, Steinbach P, Pietzsch T, Preibisch S, Tomancak P, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Christopher Schmied
    Developer

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

  2. Peter Steinbach
    Developer

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

  3. Tobias Pietzsch
    Developer

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

  4. Stephan Preibisch
    Developer

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

  5. Pavel Tomancak
    Investigator

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

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Summary
AccessionBT006559
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByPavel Tomancak