论文信息 - 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 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.

[1] Jens Rittscher,et al. Coupled Minimum-Cost Flow Cell Tracking , 2009, IPMI.

[2] J. Sulston,et al. The embryonic cell lineage of the nematode Caenorhabditis elegans. , 1983, Developmental biology.

[3] Takeo Kanade,et al. Cell population tracking and lineage construction with spatiotemporal context , 2008, Medical Image Anal..

[4] Philipp J. Keller,et al. Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[5] P. Bourgine,et al. Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy , 2010, Science.

[6] Olga Veksler,et al. Fast Approximate Energy Minimization via Graph Cuts , 2001, IEEE Trans. Pattern Anal. Mach. Intell..

[7] Yousef Al-Kofahi,et al. Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images , 2010, IEEE Transactions on Biomedical Engineering.

[8] Alessandro Sarti,et al. Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis , 2010, IEEE Transactions on Image Processing.

[9] Leo Breiman,et al. Random Forests , 2001, Machine Learning.

[10] B. Roysam,et al. Automated Cell Lineage Construction: A Rapid Method to Analyze Clonal Development Established with Murine Neural Progenitor Cells , 2006, Cell cycle.