Deltr: Digital embryo lineage tree reconstructor

Deltr: Digital embryo lineage tree reconstructor

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 com...

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Hauptverfasser: Lou, X, Kaster, F O, Lindner, M S, Kausler, B X, Kothe, U, Hockendorf, B, Wittbrodt, J, Janicke, H, Hamprecht, F A
Format: Tagungsbericht
Sprache:eng
Schlagworte:
Cell Lineage Reconstruction
Cell Tracking
Data visualization
Embryo
Image reconstruction
Image segmentation
Optimization
Pipelines
Segmentation
Shape
Shape Regularization
Visualization
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Beschreibung
Zusammenfassung: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.
ISSN:1945-7928
1945-8452
DOI:10.1109/ISBI.2011.5872698