Automatic cell lineage reconstruction Print

The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types of fluorescence microscopes, (2) scalability, by analyzing advanced stages of development with up to 20,000 cells per time point, at 26,000 cells min-1 on a single computer workstation, and (3) ease of use, by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities.


You can download the source code here or in the Keller Lab website on the software section.


Please, if you use this software in your research cite the following paper:


[1] Amat, F., Lemon, W., Mossing, D., McDole, K., Wan, Y., Branson, K. et al. (2014). Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nature Methods, 11(9), 951-958.

Last Updated on Thursday, 06 November 2014 03:03