title: Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos.
abstract: We present the Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. RACE is 55-330 times faster and 2-5 times more accurate than state-of-the-art methods. We demonstrate the generality of RACE by extracting cell-shape information from entire Drosophila, zebrafish, and mouse embryos imaged with confocal and light-sheet microscopes. Using RACE, we automatically reconstructed cellular-resolution tissue anisotropy maps across developing Drosophila embryos and quantified differences in cell-shape dynamics in wild-type and mutant embryos. We furthermore integrated RACE with our framework for automated cell lineaging and performed joint segmentation and cell tracking in entire Drosophila embryos. RACE processed these terabyte-sized datasets on a single computer within 1.4 days. RACE is easy to use, as it requires adjustment of only three parameters, takes full advantage of state-of-the-art multi-core processors and graphics cards, and is available as open-source software for Windows, Linux, and Mac OS.
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA; Karlsruhe Institute of Technology, Institute for Applied Computer Science, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. Electronic address: johannes.stegmaier@kit.edu.
authors.forename: Johannes
authors.initials: J
authors.lastname: Stegmaier
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Amat
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
authors.forename: William C
authors.initials: WC
authors.lastname: Lemon
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
authors.forename: Katie
authors.initials: K
authors.lastname: McDole
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
authors.forename: Yinan
authors.initials: Y
authors.lastname: Wan
authors.affiliation: Department of Computer Science, University of Brasilia, Campus Darcy Ribeiro, Brasília, CEP 70910-900, Brazil.
authors.forename: George
authors.initials: G
authors.lastname: Teodoro
authors.affiliation: Karlsruhe Institute of Technology, Institute for Applied Computer Science, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Mikut
authors.affiliation: Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA. Electronic address: kellerp@janelia.hhmi.org.
authors.forename: Philipp J
authors.initials: PJ
authors.lastname: Keller
mesh_terms: D000465:Algorithms; D000818:Animals; D048430:Cell Shape / Q000502:physiology*; D058948:Cell Tracking / Q000379:methods; D004330:Drosophila; D047108:Embryonic Development / Q000502:physiology*; D021621:Imaging, Three-Dimensional; D051379:Mice; D008856:Microscopy, Fluorescence / Q000379:methods; D012984:Software; D015027:Zebrafish