An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution

Andrei Y Kobitski; Jens C Otte; Masanari Takamiya; Benjamin Schäfer; Jonas Mertes; Johannes Stegmaier; Sepand Rastegar; Francesca Rindone; Volker Hartmann; Rainer Stotzka; Ariel García; Jos van Wezel; Ralf Mikut; Uwe Strähle; G Ulrich Nienhaus

doi:10.1038/srep08601

An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution

Sci Rep. 2015 Feb 25:5:8601. doi: 10.1038/srep08601.

Authors

Affiliations

¹ 1] Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany [2] Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany [3] European Zebrafish Resource Centre, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany.
² 1] Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany [2] European Zebrafish Resource Centre, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany.
³ Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.
⁴ Institute for Applied Computer Science, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany.
⁵ Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany.
⁶ Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany.
⁷ Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
⁸ 1] Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany [2] Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany [3] European Zebrafish Resource Centre, Karlsruhe Institute of Technology, Post Office Box 3640, 76021 Karlsruhe, Germany [4] Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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 16 h 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.

Publication types

Research Support, Non-U.S. Gov't

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