
Reconstruction of cell lineages from large-scale fluorescence microscopy data - mrfusion
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3036.html
======
irickt
Abstract: 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 the segmentation and tracking of
cell nuclei with high accuracy and speed. We demonstrate its (i) generality by
reconstructing cell lineages in four-dimensional, terabyte-sized image data
sets of fruit fly, zebrafish and mouse embryos acquired with three types of
fluorescence microscopes, (ii) 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 (iii) 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. Using our system, we
performed the first cell lineage reconstruction of early Drosophila
melanogaster nervous system development, revealing neuroblast dynamics
throughout an entire embryo.

There are a lot of supplementary materials including video and software. But
the text will cost you $32.

