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

Developmental Cell
Johannes StegmaierPhilipp J Keller

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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Citations

Mar 24, 2016·Developmental Cell·Zhe Liu, Philipp J Keller
Jul 2, 2016·BMC Developmental Biology·Johannes GirstmairMaximilian J Telford
Nov 9, 2016·Nature Biotechnology·Stavroula SkylakiTimm Schroeder
Jun 9, 2016·PLoS Computational Biology·Yu ToyoshimaYuichi Iino
Jun 20, 2017·Development, Growth & Differentiation·Koichiro Uriu, Luis G Morelli
Feb 16, 2018·Development·Yara E Sánchez-CorralesVerônica A Grieneisen
Aug 16, 2017·Proceedings of the National Academy of Sciences of the United States of America·Weizhe LiMichael Y Gerner
Feb 2, 2019·PloS One·Tristan A SharpAndrea J Liu
Feb 13, 2019·PLoS Computational Biology·Damien G HicksSarah M Russell
May 6, 2019·Current Protocols in Cell Biology·Jesse AaronTeng-Leong Chew
Feb 1, 2020·Wiley Interdisciplinary Reviews. Developmental Biology·Chase C WesleyDaniel L Levy
Apr 7, 2020·ELife·Alexandra SchauerCarl-Philipp Heisenberg
Jun 25, 2020·PLoS Computational Biology·Jakob RosenbauerAlexander Schug
Aug 25, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Karolis LeonaviciusShankar Srinivas
Oct 4, 2019·Nature Communications·Cody J Greer, Timothy E Holy
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Feb 9, 2017·The Journal of Cell Biology·Shaohe WangKenneth M Yamada
Aug 25, 2018·Scientific Reports·James McCollAndrea Münsterberg
Jul 13, 2019·Annual Review of Cell and Developmental Biology·Yinan WanPhilipp J Keller
Apr 10, 2019·BMC Bioinformatics·Jianfeng CaoHong Yan
Mar 30, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alexandre C DufourJean-Christophe Olivo-Marin
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Jan 5, 2019·BMC Bioinformatics·Sarah MachadoNicolas Chiaruttini
Aug 10, 2016·Journal of Cell Science·Gautier FollainJacky G Goetz
Oct 28, 2018·Nature Protocols·Loïc A RoyerPhilipp J Keller
Jun 30, 2019·Nature Communications·Bruno LeggioEmmanuel Faure
Jul 3, 2020·Computational and Structural Biotechnology Journal·Filippo PiccininiPeter Horvath
Nov 6, 2020·Nature Communications·Philipp D LöselVincent Heuveline
Jul 14, 2019·Cellular Immunology·Nazihah HusnaYingrou Tan
Apr 11, 2021·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Sharada IyerMegha Kumar

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