%0 Journal Article %1 amat2014accurate %A Amat, Fernando %A Lemon, William %A Mossing, Daniel P %A McDole, Katie %A Wan, Yinan %A Branson, Kristin %A Myers, Eugene W %A Keller, Philipp J %D 2014 %I Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. %J Nat Meth %K biology cells microscopy of_applications optical_flow segmentation software to_READ tracking zebrafish %N 9 %P 951--958 %T Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data %U http://dx.doi.org/10.1038/nmeth.3036 %V 11 %X 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.

@article{amat2014accurate, 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.}, added-at = {2014-10-01T15:48:27.000+0200}, author = {Amat, Fernando and Lemon, William and Mossing, Daniel P and McDole, Katie and Wan, Yinan and Branson, Kristin and Myers, Eugene W and Keller, Philipp J}, biburl = {https://www.bibsonomy.org/bibtex/2b86b031b6b08390c1c26513832a494a9/alex_ruff}, description = {Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data : Nature Methods : Nature Publishing Group}, interhash = {92c17ca625238666f2e7662aafdbcdd1}, intrahash = {b86b031b6b08390c1c26513832a494a9}, issn = {15487091}, journal = {Nat Meth}, keywords = {biology cells microscopy of_applications optical_flow segmentation software to_READ tracking zebrafish}, month = sep, number = 9, pages = {951--958}, publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, timestamp = {2014-10-01T16:09:54.000+0200}, title = {Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data}, url = {http://dx.doi.org/10.1038/nmeth.3036}, volume = 11, year = 2014 }