4D embryogenesis image analysis using PDE methods of image processing

Title:

4D embryogenesis image analysis using PDE methods of image processing

Creator:

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

Identifier:

https://cdk.lib.cas.cz/client/handle/uuid:be578edb-c0f4-48df-8044-815c0913b797
uuid:be578edb-c0f4-48df-8044-815c0913b797

Subject:

image processing, embryogenesis, image analysis, finite volume method, image filtering, object counting, segmentation, and partial differential equation

Type:

model:article and TEXT

Format:

bez média and svazek

Description:

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.

Language:

English

Rights:

http://creativecommons.org/publicdomain/mark/1.0/
policy:public

Coverage:

[226]-259

Source:

Kybernetika | 2010 Volume:46 | Number:2

Harvested from:

CDK

Metadata only:

false