Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos.

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Developmental Cell. 2016 Jan 25;36(2):225-40. doi: 10.1016/j.devcel.2015.12.028

Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos. Keller Lab

Stegmaier J, Amat F, Lemon WC, McDole K, Wan Y, Teodoro G, Mikut R, Keller PJ

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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.

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Real-time three-dimensional cell segmentation in large-scale microscopy data of developing embryos.

Abstract

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