17
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      An automated workflow for parallel processing of large multiview SPIM recordings

      Preprint

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Multiview light sheet fluorescence microscopy (LSFM) 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 cluster (HPC). Here we introduce an automated workflow for processing large multiview, multi-channel, multi-illumination time-lapse LSFM data on a single workstation or in parallel on a HPC. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing LSFM data in a fraction of the time required to collect it.

          Related collections

          Most cited references4

          • Record: found
          • Abstract: found
          • Article: not found

          Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy.

          A long-standing goal of biology is to map the behavior of all cells during vertebrate embryogenesis. We developed digital scanned laser light sheet fluorescence microscopy and recorded nuclei localization and movement in entire wild-type and mutant zebrafish embryos over the first 24 hours of development. Multiview in vivo imaging at 1.5 billion voxels per minute provides "digital embryos," that is, comprehensive databases of cell positions, divisions, and migratory tracks. Our analysis of global cell division patterns reveals a maternally defined initial morphodynamic symmetry break, which identifies the embryonic body axis. We further derive a model of germ layer formation and show that the mesendoderm forms from one-third of the embryo's cells in a single event. Our digital embryos, with 55 million nucleus entries, are provided as a resource.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Computing for the Large Hadron Collider

            Ian Bird (2011)
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

                Bookmark

                Author and article information

                Journal
                2015-07-30
                2015-08-11
                Article
                1507.08575
                646db9ab-409a-4d0b-b396-7a4efb87006c

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

                History
                Custom metadata
                13 pages with supplement, LATEX; 1 table, 1 figure, 2 supplementary figures, 2 supplementary lists, 2 supplementary tables; corrected error in results table, results unchanged
                q-bio.QM

                Quantitative & Systems biology
                Quantitative & Systems biology

                Comments

                Comment on this article