Deltr: Digital embryo lineage tree reconstructor

Author

Lou, X. ; Kaster, F.O. ; Lindner, M.S. ; Kausler, B.X. ; Köthe, U. ; Höckendorf, B. ; Wittbrodt, J. ; Jänicke, H. ; Hamprecht, F.A.

Author_Institution

Interdiscipl. Center for Sci. Comput., Univ. of Heidelberg, Heidelberg, Germany

fYear

2011

fDate

March 30 2011-April 2 2011

Firstpage

1557

Lastpage

1560

Abstract

We present DELTR, an automated pipeline for the analysis of time-resolved light sheet fluorescence microscopy images of zebrafish embryogenesis. It comprises 3D nucleus segmentation using shape-regularized graph cuts, parallelized extraction of geometrical features, and cell tracking by means of combinatorial optimization. We also discuss the interactive visualization software used for validating the results, and describe our advances towards reconstructing the entire cell lineage tree of the zebrafish. Our method achieves ca. 96 % accuracy for cell nucleus detection and ca. 90 % accuracy for the association of nuclei across subsequent time steps.

Keywords

biological techniques; biology computing; cellular biophysics; feature extraction; fluorescence; image reconstruction; image segmentation; optical microscopy; optimisation; zoology; 3D nucleus segmentation; DELTR; cell tracking; combinatorial optimization; digital embryo lineage tree reconstructor; interactive visualization software; parallelized geometrical feature extraction; shape-regularized graph cuts; time-resolved light sheet fluorescence microscopy images; zebrafish embryogenesis; Data visualization; Embryo; Image reconstruction; Image segmentation; Optimization; Pipelines; Shape; Cell Lineage Reconstruction; Cell Tracking; Segmentation; Shape Regularization; Visualization;

fLanguage

English

Publisher

ieee

Conference_Titel

Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on

Conference_Location

Chicago, IL

ISSN

1945-7928

Print_ISBN

978-1-4244-4127-3

Electronic_ISBN

1945-7928

Type

conf

DOI

10.1109/ISBI.2011.5872698

Filename

5872698