title: Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data.
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.
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Amat
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: William
authors.identifier: 000000034541738X
authors.initials: W
authors.lastname: Lemon
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Mossing
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Katie
authors.initials: K
authors.lastname: McDole
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Yinan
authors.initials: Y
authors.lastname: Wan
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Branson
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Myers
authors.affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Philipp J
authors.initials: PJ
authors.lastname: Keller
mesh_terms: D000818:Animals; D019070:Cell Lineage / Q000502:physiology*; D058948:Cell Tracking / Q000379:methods*; D002478:Cells, Cultured; D057225:Data Mining / Q000379:methods; D004330:Drosophila; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software; D013234:Stem Cells / Q000166:cytology* / Q000502:physiology*; D014584:User-Computer Interface; D015027:Zebrafish