Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging

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

doi:10.1109/ISBI.2011.5872699

Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging

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

Universidad Politécnica de Madrid
Ecole Polytechnique
Centre national de la recherche scientifique
Institut Polytechnique de Paris

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and m spatial resolution [1].

Original language	English
Title of host publication	2011 8th IEEE International Symposium on Biomedical Imaging
Subtitle of host publication	From Nano to Macro, ISBI'11
Publisher	IEEE Computer Society
Pages	1561-1564
Number of pages	4
ISBN (Print)	9781424441280
DOIs	https://doi.org/10.1109/ISBI.2011.5872699
Publication status	Published - 1 Jan 2011
Event	8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011 - Chicago, IL, United States Duration: 30 Mar 2011 → 2 Apr 2011

Publication series

Name	Proceedings - International Symposium on Biomedical Imaging
ISSN (Print)	1945-7928
ISSN (Electronic)	1945-8452

Conference

Conference	8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011
Country/Territory	United States
City	Chicago, IL
Period	30/03/11 → 2/04/11

Keywords

in-vivo imaging
lineage tree
multiphoton microscopy
viscous watershed
zebrafish development

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10.1109/ISBI.2011.5872699

Cite this

Luengo-Oroz, M. A., Savy, T., Rubio, J. L., Duloquin, L., Faure, E., Olivier, N., Ledesma-Carbayo, M., Debarre, D., Bourgine, P., Beaurepaire, E., Peyrieras, N., & Santos, A. (2011). Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. In 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 (pp. 1561-1564). Article 5872699 (Proceedings - International Symposium on Biomedical Imaging). IEEE Computer Society. https://doi.org/10.1109/ISBI.2011.5872699

Luengo-Oroz, Miguel A. ; Savy, Thierry ; Rubio, Jose L. et al. / Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. IEEE Computer Society, 2011. pp. 1561-1564 (Proceedings - International Symposium on Biomedical Imaging).

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title = "Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging",

abstract = "The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and m spatial resolution [1].",

keywords = "in-vivo imaging, lineage tree, multiphoton microscopy, viscous watershed, zebrafish development",

author = "Luengo-Oroz, \{Miguel A.\} and Thierry Savy and Rubio, \{Jose L.\} and Louise Duloquin and Emmanuel Faure and Nicolas Olivier and Maria Ledesma-Carbayo and Delphine Debarre and Paul Bourgine and Emmanuel Beaurepaire and Nadine Peyrieras and Andres Santos",

year = "2011",

month = jan,

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doi = "10.1109/ISBI.2011.5872699",

language = "English",

isbn = "9781424441280",

series = "Proceedings - International Symposium on Biomedical Imaging",

publisher = "IEEE Computer Society",

pages = "1561--1564",

booktitle = "2011 8th IEEE International Symposium on Biomedical Imaging",

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Luengo-Oroz, MA, Savy, T, Rubio, JL, Duloquin, L, Faure, E, Olivier, N, Ledesma-Carbayo, M, Debarre, D, Bourgine, P, Beaurepaire, E, Peyrieras, N & Santos, A 2011, Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. in 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11., 5872699, Proceedings - International Symposium on Biomedical Imaging, IEEE Computer Society, pp. 1561-1564, 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011, Chicago, IL, United States, 30/03/11. https://doi.org/10.1109/ISBI.2011.5872699

Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. / Luengo-Oroz, Miguel A.; Savy, Thierry; Rubio, Jose L. et al.
2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. IEEE Computer Society, 2011. p. 1561-1564 5872699 (Proceedings - International Symposium on Biomedical Imaging).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Luengo-Oroz, Miguel A.

AU - Savy, Thierry

AU - Rubio, Jose L.

AU - Duloquin, Louise

AU - Faure, Emmanuel

AU - Olivier, Nicolas

AU - Ledesma-Carbayo, Maria

AU - Debarre, Delphine

AU - Bourgine, Paul

AU - Beaurepaire, Emmanuel

AU - Peyrieras, Nadine

AU - Santos, Andres

PY - 2011/1/1

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N2 - The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and m spatial resolution [1].

AB - The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and m spatial resolution [1].

KW - in-vivo imaging

KW - lineage tree

KW - multiphoton microscopy

KW - viscous watershed

KW - zebrafish development

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M3 - Conference contribution

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BT - 2011 8th IEEE International Symposium on Biomedical Imaging

PB - IEEE Computer Society

T2 - 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011

Y2 - 30 March 2011 through 2 April 2011

ER -

Luengo-Oroz MA, Savy T, Rubio JL, Duloquin L, Faure E, Olivier N et al. Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. In 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. IEEE Computer Society. 2011. p. 1561-1564. 5872699. (Proceedings - International Symposium on Biomedical Imaging). doi: 10.1109/ISBI.2011.5872699

Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging

Abstract

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Keywords

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