PUBLICATION

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

Authors
Schott, B., Traub, M., Schlagenhauf, C., Takamiya, M., Antritter, T., Bartschat, A., Löffler, K., Blessing, D., Otte, J.C., Kobitski, A.Y., Nienhaus, G.U., Strähle, U., Mikut, R., Stegmaier, J.
ID
ZDB-PUB-180421-10
Date
2018
Source
PLoS Computational Biology   14: e1006128 (Journal)
Registered Authors
Mikut, Ralf, Otte, Jens, Strähle, Uwe, Takamiya, Masanari
Keywords
none
MeSH Terms
  • Olfactory Mucosa/cytology
  • Olfactory Mucosa/embryology
  • Computational Biology
  • Microscopy, Fluorescence
  • Imaging, Three-Dimensional
  • Gastrulation
  • Cell Tracking/statistics & numerical data*
  • Animals
  • Cell Movement
  • Zebrafish/embryology*
  • Germ Layers/cytology
  • Embryonic Stem Cells/cytology
  • Software
  • Animals, Genetically Modified
  • Embryonic Development
(all 15)
PubMed
29672531 Full text @ PLoS Comput. Biol.
Abstract
State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.
Genes / Markers
Marker Marker Type Name
h2az2aGENEH2A.Z variant histone 2a
sox10GENESRY-box transcription factor 10
1 - 2 of 2
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Figures
Figure Gallery (7 images)
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Expression
No data available
Phenotype
No data available
Mutations / Transgenics
Allele Construct Type Affected Genomic Region
ka96TgTransgenic Insertion
    kca66TgTransgenic Insertion
      1 - 2 of 2
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      Human Disease / Model
      No data available
      Sequence Targeting Reagents
      No data available
      Fish
      No data available
      Antibodies
      No data available
      Orthology
      No data available
      Engineered Foreign Genes
      Marker Marker Type Name
      EosEFGEos
      GFPEFGGFP
      1 - 2 of 2
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      Mapping
      No data available
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      Citation
      Schott, B., Traub, M., Schlagenhauf, C., Takamiya, M., Antritter, T., Bartschat, A., Löffler, K., Blessing, D., Otte, J.C., Kobitski, A.Y., Nienhaus, G.U., Strähle, U., Mikut, R., Stegmaier, J. (2018) EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. PLoS Computational Biology. 14:e1006128.