期刊
DEVELOPMENTAL CELL
卷 36, 期 2, 页码 225-240出版社
CELL PRESS
DOI: 10.1016/j.devcel.2015.12.028
关键词
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资金
- Howard Hughes Medical Institute
- Helmholtz Association in the Program Bio-Interfaces
- Karlsruhe House of Young Scientists
- Brazilian National Council for Scientific and Technological Development (CNPq)
d 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 55330 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.
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