Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy.

Miguel A Luengo-Oroz; Jose L Rubio-Guivernau; Emmanuel Faure; Thierry Savy; Louise Duloquin; Nicolas Olivier; David Pastor; Maria Ledesma-Carbayo; Delphine Debarre; Paul Bourgine; Emmanuel Beaurepaire; Nadine Peyrieras; Andres Santos

hal-00683640, version 1

Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy.

Miguel A Luengo-Oroz ¹, Jose L Rubio-Guivernau, Emmanuel Faure ², Thierry Savy ², Louise Duloquin ^3, 4, Nicolas Olivier ⁵, David Pastor, Maria Ledesma-Carbayo, Delphine Debarre ⁶, Paul Bourgine ^2, 7, Emmanuel Beaurepaire () ⁵, Nadine Peyrieras ^3, 4, 8, Andres Santos ⁹

IEEE Transactions on Image Processing 21, 4 (2012) 2335-40

Abstract: Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.

1: Biomedical Image Technologies, Biomedical Research Center (CIBER-BBN)
Universidad Politécnica de Madrid
2: Centre de recherche en épistémologie appliquée (CREA)
CNRS : UMR7656 – Polytechnique - X
3: Neurobiologie et Développement (N&eD)
CNRS : UPR3294 – Université Paris XI - Paris Sud
4: Institut de Neurobiologie Alfred Fessard (INAF)
CNRS : FRC2118
5: Laboratoire d'optique et biosciences (LOB)
CNRS : UMR7645 – INSERM : U696 – Polytechnique - X
6: Laboratoire Interdisciplinaire de Physique (LIPhy)
CNRS : UMR5588 – Université Joseph Fourier - Grenoble I
7: Réseau National des Systèmes Complexes (RNSC)
CNRS : UMR0 – INSERM : U0 – Institut national de la recherche agronomique (INRA) : UMR0 – Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) – Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR0 – INRIA – Institut de recherche pour le développement [IRD] – CGE – CPU
8: Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF)
CNRS : UMR7656 – Institut Curie – Université Paris XI - Paris Sud – Université Paris I - Panthéon-Sorbonne – Université Pierre et Marie Curie [UPMC] - Paris VI – École normale supérieure de Cachan - ENS Cachan – Ecole normale supérieure de Paris - ENS Paris – Polytechnique - X
9: Physics
University of Extremadura

hal-00683640, version 1
http://hal.archives-ouvertes.fr/hal-00683640
oai:hal.archives-ouvertes.fr:hal-00683640
From: Alain Perignon <>
Submitted on: Thursday, 29 March 2012 14:26:46
Updated on: Thursday, 29 March 2012 14:26:46

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PubMed: 22155959

DOI: 10.1109/TIP.2011.2177911

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%% hal-00683640, version 1
%% http://hal.archives-ouvertes.fr/hal-00683640
@article{luengooroz:hal-00683640,
    hal_id = {hal-00683640},
    url = {http://hal.archives-ouvertes.fr/hal-00683640},
    title = {{Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy.}},
    author = {Luengo-Oroz, Miguel A and Rubio-Guivernau, Jose L and Faure, Emmanuel and Savy, Thierry and Duloquin, Louise and Olivier, Nicolas and Pastor, David and Ledesma-Carbayo, Maria and Debarre, Delphine and Bourgine, Paul and Beaurepaire, Emmanuel and Peyrieras, Nadine and Santos, Andres},
    abstract = {{Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.}},
    language = {English},
    affiliation = {Biomedical Image Technologies, Biomedical Research Center - CIBER-BBN , Centre de recherche en {\'e}pist{\'e}mologie appliqu{\'e}e - CREA , Neurobiologie et D{\'e}veloppement - N\&eD , Institut de Neurobiologie Alfred Fessard - INAF , Laboratoire d'optique et biosciences - LOB , Laboratoire Interdisciplinaire de Physique - LIPhy , R{\'e}seau National des Syst{\`e}mes Complexes - RNSC , Institut des Syst{\`e}mes Complexes - Paris Ile-de-France - ISC-PIF , Physics},
    pages = {2335-40},
    journal = {IEEE Transactions on Image Processing},
    volume = {21},
    number = {4 },
    audience = {international },
    doi = {10.1109/TIP.2011.2177911 },
    year = {2012},
    month = Apr,
}

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