Cells segmentation from 3-D confocal images of early zebrafish embryogenesis

We designed a strategy for extracting the shapes of cell membranes and nuclei from time lapse confocal images taken throughout early zebrafish embryogenesis using a partial-differential-equation-based segmentation. This segmentation step is a prerequisite for an accurate quantitative analysis of cel...

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Autores principales:	Zanella, C., Campana, M., Rizzi, B., Melani, C., Sanguinetti, G., Bourgine, P., Mikula, K., Peyrieras, N., Sarti, A.
Formato:	JOUR
Materias:	Bioimaging Confocal imaging Image processing Segmentation Subjective surfaces Algorithm validation Automated algorithms Bio-imaging Biological process Cell shapes Classical methods Confocal image Edge preserving Embryonic cells Image features Morphodynamics Quantitative analysis Sub-cellular Zebrafish Zebrafish embryos Cell membranes Cytology Imaging systems Signal to noise ratio Three dimensional Edge detection algorithm animal animal embryo article cell division cell membrane cell nucleus cell shape cytology image processing methodology prenatal development reproducibility zebra fish Algorithms Animals Cell Division Cell Membrane Cell Nucleus Cell Shape Embryo, Nonmammalian Image Processing, Computer-Assisted Reproducibility of Results
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_10577149_v19_n3_p770_Zanella
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_10577149_v19_n3_p770_Zanella
record_format	dspace
spelling	todo:paper_10577149_v19_n3_p770_Zanella2023-10-03T16:00:55Z Cells segmentation from 3-D confocal images of early zebrafish embryogenesis Zanella, C. Campana, M. Rizzi, B. Melani, C. Sanguinetti, G. Bourgine, P. Mikula, K. Peyrieras, N. Sarti, A. Bioimaging Confocal imaging Image processing Segmentation Subjective surfaces Algorithm validation Automated algorithms Bio-imaging Biological process Cell shapes Classical methods Confocal image Confocal imaging Edge preserving Embryonic cells Image features Morphodynamics Quantitative analysis Sub-cellular Zebrafish Zebrafish embryos Cell membranes Cytology Image processing Imaging systems Signal to noise ratio Three dimensional Edge detection algorithm animal animal embryo article cell division cell membrane cell nucleus cell shape cytology image processing methodology prenatal development reproducibility zebra fish Algorithms Animals Cell Division Cell Membrane Cell Nucleus Cell Shape Embryo, Nonmammalian Image Processing, Computer-Assisted Reproducibility of Results Zebrafish We designed a strategy for extracting the shapes of cell membranes and nuclei from time lapse confocal images taken throughout early zebrafish embryogenesis using a partial-differential-equation-based segmentation. This segmentation step is a prerequisite for an accurate quantitative analysis of cell morphodynamics during embryogenesis and it is the basis for an integrated understanding of biological processes. The segmentation of embryonic cells requires live zebrafish embryos fluorescently labeled to highlight sub-cellular structures and designing specific algorithms by adapting classical methods to image features. Our strategy includes the following steps: the signal-to-noise ratio is first improved by an edge-preserving filtering, then the cell shape is reconstructed applying a fully automated algorithm based on a generalized version of the Subjective Surfaces technique. Finally we present a procedure for the algorithm validation either from the accuracy and the robustness perspective. © 2010 IEEE. Fil:Melani, C. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_10577149_v19_n3_p770_Zanella
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Bioimaging Confocal imaging Image processing Segmentation Subjective surfaces Algorithm validation Automated algorithms Bio-imaging Biological process Cell shapes Classical methods Confocal image Confocal imaging Edge preserving Embryonic cells Image features Morphodynamics Quantitative analysis Sub-cellular Zebrafish Zebrafish embryos Cell membranes Cytology Image processing Imaging systems Signal to noise ratio Three dimensional Edge detection algorithm animal animal embryo article cell division cell membrane cell nucleus cell shape cytology image processing methodology prenatal development reproducibility zebra fish Algorithms Animals Cell Division Cell Membrane Cell Nucleus Cell Shape Embryo, Nonmammalian Image Processing, Computer-Assisted Reproducibility of Results Zebrafish
spellingShingle	Bioimaging Confocal imaging Image processing Segmentation Subjective surfaces Algorithm validation Automated algorithms Bio-imaging Biological process Cell shapes Classical methods Confocal image Confocal imaging Edge preserving Embryonic cells Image features Morphodynamics Quantitative analysis Sub-cellular Zebrafish Zebrafish embryos Cell membranes Cytology Image processing Imaging systems Signal to noise ratio Three dimensional Edge detection algorithm animal animal embryo article cell division cell membrane cell nucleus cell shape cytology image processing methodology prenatal development reproducibility zebra fish Algorithms Animals Cell Division Cell Membrane Cell Nucleus Cell Shape Embryo, Nonmammalian Image Processing, Computer-Assisted Reproducibility of Results Zebrafish Zanella, C. Campana, M. Rizzi, B. Melani, C. Sanguinetti, G. Bourgine, P. Mikula, K. Peyrieras, N. Sarti, A. Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
topic_facet	Bioimaging Confocal imaging Image processing Segmentation Subjective surfaces Algorithm validation Automated algorithms Bio-imaging Biological process Cell shapes Classical methods Confocal image Confocal imaging Edge preserving Embryonic cells Image features Morphodynamics Quantitative analysis Sub-cellular Zebrafish Zebrafish embryos Cell membranes Cytology Image processing Imaging systems Signal to noise ratio Three dimensional Edge detection algorithm animal animal embryo article cell division cell membrane cell nucleus cell shape cytology image processing methodology prenatal development reproducibility zebra fish Algorithms Animals Cell Division Cell Membrane Cell Nucleus Cell Shape Embryo, Nonmammalian Image Processing, Computer-Assisted Reproducibility of Results Zebrafish
description	We designed a strategy for extracting the shapes of cell membranes and nuclei from time lapse confocal images taken throughout early zebrafish embryogenesis using a partial-differential-equation-based segmentation. This segmentation step is a prerequisite for an accurate quantitative analysis of cell morphodynamics during embryogenesis and it is the basis for an integrated understanding of biological processes. The segmentation of embryonic cells requires live zebrafish embryos fluorescently labeled to highlight sub-cellular structures and designing specific algorithms by adapting classical methods to image features. Our strategy includes the following steps: the signal-to-noise ratio is first improved by an edge-preserving filtering, then the cell shape is reconstructed applying a fully automated algorithm based on a generalized version of the Subjective Surfaces technique. Finally we present a procedure for the algorithm validation either from the accuracy and the robustness perspective. © 2010 IEEE.
format	JOUR
author	Zanella, C. Campana, M. Rizzi, B. Melani, C. Sanguinetti, G. Bourgine, P. Mikula, K. Peyrieras, N. Sarti, A.
author_facet	Zanella, C. Campana, M. Rizzi, B. Melani, C. Sanguinetti, G. Bourgine, P. Mikula, K. Peyrieras, N. Sarti, A.
author_sort	Zanella, C.
title	Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
title_short	Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
title_full	Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
title_fullStr	Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
title_full_unstemmed	Cells segmentation from 3-D confocal images of early zebrafish embryogenesis
title_sort	cells segmentation from 3-d confocal images of early zebrafish embryogenesis
url	http://hdl.handle.net/20.500.12110/paper_10577149_v19_n3_p770_Zanella
work_keys_str_mv	AT zanellac cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT campanam cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT rizzib cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT melanic cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT sanguinettig cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT bourginep cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT mikulak cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT peyrierasn cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis AT sartia cellssegmentationfrom3dconfocalimagesofearlyzebrafishembryogenesis
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Cells segmentation from 3-D confocal images of early zebrafish embryogenesis

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