ZFIN ID: ZDB-PUB-150226-8
An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution
Kobitski, A.Y., Otte, J.C., Takamiya, M., Schäfer, B., Mertes, J., Stegmaier, J., Rastegar, S., Rindone, F., Hartmann, V., Stotzka, R., García, A., van Wezel, J., Mikut, R., Strähle, U., Nienhaus, G.U.
Date: 2015
Source: Scientific Reports   5: 8601 (Journal)
Registered Authors: Mikut, Ralf, Nienhaus, Chris, Otte, Jens, Rastegar, Sepand, Strähle, Uwe, Takamiya, Masanari
Keywords: Light-sheet microscopy, Biological fluorescence
MeSH Terms:
  • Animals
  • Cell Count
  • Data Mining
  • Datasets as Topic
  • Embryo, Nonmammalian*
  • Embryonic Development*/genetics
  • Image Interpretation, Computer-Assisted
  • Image Processing, Computer-Assisted
  • Microscopy, Fluorescence/methods*
  • Microscopy, Fluorescence/standards
  • Morphogenesis
  • Mutation
  • Zebrafish*/genetics
PubMed: 25712513 Full text @ Sci. Rep.
A new era in developmental biology has been ushered in by recent advances in the quantitative imaging of all-cell morphogenesis in living organisms. Here we have developed a light-sheet fluorescence microscopy-based framework with single-cell resolution for identification and characterization of subtle phenotypical changes of millimeter-sized organisms. Such a comparative study requires analyses of entire ensembles to be able to distinguish sample-to-sample variations from definitive phenotypical changes. We present a kinetic digital model of zebrafish embryos up to 16h of development. The model is based on the precise overlay and averaging of data taken on multiple individuals and describes the cell density and its migration direction at every point in time. Quantitative metrics for multi-sample comparative studies have been introduced to analyze developmental variations within the ensemble. The digital model may serve as a canvas on which the behavior of cellular subpopulations can be studied. As an example, we have investigated cellular rearrangements during germ layer formation at the onset of gastrulation. A comparison of the one-eyed pinhead (oep) mutant with the digital model of the wild-type embryo reveals its abnormal development at the onset of gastrulation, many hours before changes are obvious to the eye.