Title :
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
fDate :
March 30 2011-April 2 2011
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;
Conference_Titel :
Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on
Conference_Location :
Chicago, IL
Print_ISBN :
978-1-4244-4127-3
Electronic_ISBN :
1945-7928
DOI :
10.1109/ISBI.2011.5872698
