# 4D Embryogenesis image analysis using PDE methods of image processing

Paul Bourgine; Róbert Čunderlík; Olga Drblíková-Stašová; Karol Mikula; Mariana Remešíková; Nadine Peyriéras; Barbara Rizzi; Alessandro Sarti

Kybernetika (2010)

- Volume: 46, Issue: 2, page 226-259
- ISSN: 0023-5954

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topBourgine, Paul, et al. "4D Embryogenesis image analysis using PDE methods of image processing." Kybernetika 46.2 (2010): 226-259. <http://eudml.org/doc/196413>.

@article{Bourgine2010,

abstract = {In this paper, we introduce a set of methods for processing and analyzing long time series of 3D images representing embryo evolution. The images are obtained by in vivo scanning using a confocal microscope where one of the channels represents the cell nuclei and the other one the cell membranes. Our image processing chain consists of three steps: image filtering, object counting (center detection) and segmentation. The corresponding methods are based on numerical solution of nonlinear PDEs, namely the geodesic mean curvature flow model, flux-based level set center detection and generalized subjective surface equation. All three models have a similar character and therefore can be solved using a common approach. We explain in details our semi-implicit time discretization and finite volume space discretization. This part is concluded by a short description of parallelization of the algorithms. In the part devoted to experiments, we provide the experimental order of convergence of the numerical scheme, the validation of the methods and numerous experiments with the data representing an early developmental stage of a zebrafish embryo.},

author = {Bourgine, Paul, Čunderlík, Róbert, Drblíková-Stašová, Olga, Mikula, Karol, Remešíková, Mariana, Peyriéras, Nadine, Rizzi, Barbara, Sarti, Alessandro},

journal = {Kybernetika},

keywords = {image processing; embryogenesis; image analysis; finite volume method; image filtering; object counting; segmentation; partial differential equation; finite volume method; image processing; embryogenesis; image analysis; image filtering; object counting; segmentation; partial differential equation},

language = {eng},

number = {2},

pages = {226-259},

publisher = {Institute of Information Theory and Automation AS CR},

title = {4D Embryogenesis image analysis using PDE methods of image processing},

url = {http://eudml.org/doc/196413},

volume = {46},

year = {2010},

}

TY - JOUR

AU - Bourgine, Paul

AU - Čunderlík, Róbert

AU - Drblíková-Stašová, Olga

AU - Mikula, Karol

AU - Remešíková, Mariana

AU - Peyriéras, Nadine

AU - Rizzi, Barbara

AU - Sarti, Alessandro

TI - 4D Embryogenesis image analysis using PDE methods of image processing

JO - Kybernetika

PY - 2010

PB - Institute of Information Theory and Automation AS CR

VL - 46

IS - 2

SP - 226

EP - 259

AB - In this paper, we introduce a set of methods for processing and analyzing long time series of 3D images representing embryo evolution. The images are obtained by in vivo scanning using a confocal microscope where one of the channels represents the cell nuclei and the other one the cell membranes. Our image processing chain consists of three steps: image filtering, object counting (center detection) and segmentation. The corresponding methods are based on numerical solution of nonlinear PDEs, namely the geodesic mean curvature flow model, flux-based level set center detection and generalized subjective surface equation. All three models have a similar character and therefore can be solved using a common approach. We explain in details our semi-implicit time discretization and finite volume space discretization. This part is concluded by a short description of parallelization of the algorithms. In the part devoted to experiments, we provide the experimental order of convergence of the numerical scheme, the validation of the methods and numerous experiments with the data representing an early developmental stage of a zebrafish embryo.

LA - eng

KW - image processing; embryogenesis; image analysis; finite volume method; image filtering; object counting; segmentation; partial differential equation; finite volume method; image processing; embryogenesis; image analysis; image filtering; object counting; segmentation; partial differential equation

UR - http://eudml.org/doc/196413

ER -

## References

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