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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.; Garcia, A.; van Wezel, J.; Mikut, R.; Strähle, U.; Nienhaus, G.U.

Abstract:
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.

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Volltext §
DOI: 10.5445/IR/1000045934
Originalveröffentlichung
DOI: 10.1038/srep08601
Scopus
Zitationen: 16
Web of Science
Zitationen: 17
Coverbild
Zugehörige Institution(en) am KIT Institut für Angewandte Physik (APH)
Steinbuch Centre for Computing (SCC)
Institut für Toxikologie und Genetik (ITG)
Institut für Angewandte Informatik (IAI)
Institut für Nanotechnologie (INT)
Institut für Prozessdatenverarbeitung und Elektronik (IPE)
Publikationstyp Zeitschriftenaufsatz
Jahr 2015
Sprache Englisch
Identifikator ISSN: 2045-2322
urn:nbn:de:swb:90-459343
KITopen-ID: 1000045934
HGF-Programm 47.01.01 (POF III, LK 01)
Erschienen in Scientific Reports
Band 5
Heft 8601
Seiten 1-10
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
Schlagworte Light-sheet microscopy, Biological fluorescence
Nachgewiesen in Scopus
Web of Science
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