Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

• Published in: Developmental cell 2016-01, Vol.36 (2), p.225-240
• Main Authors: Stegmaier, Johannes, Amat, Fernando, Lemon, William C., McDole, Katie, Wan, Yinan, Teodoro, George, Mikut, Ralf, Keller, Philipp J.
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Cell Shape - physiology; Cell Tracking - methods; Drosophila; Embryonic Development - physiology; Imaging, Three-Dimensional; Mice; Microscopy, Fluorescence - methods; Software; Zebrafish
• ISSN: 1534-5807; 1878-1551
• DOI: 10.1016/j.devcel.2015.12.028

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. [Display omitted] •RACE framework automates 3D cell segmentation in entire fly, fish, and mouse embryos•RACE is 55–330 times faster and 2–5 times more accurate than state-of-the-art methods•RACE quantifies differences in cellular dynamics in wild-type and mutant embryos•RACE + TGMM enable joint segmentation and cell tracking in entire developing embryos Stegmaier et al. present the open-source software RACE for automated three-dimensional cell segmentation in large-scale microscopy images. RACE rapidly reconstructs cell shapes in entire developing Drosophila, zebrafish, and mouse embryos imaged with confocal or light-sheet microscopy and quantifies cell-shape dynamics and phenotypic differences in wild-type and mutant embryos.