Real Time Three Dimensional Cell Segmentation in Large Scale Microscopy Data of Developing Embryos.
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.
Developmental cell