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Deep learning is widely applicable to phenotyping embryonic development and disease

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Item Type:Article
Title:Deep learning is widely applicable to phenotyping embryonic development and disease
Creators Name:Naert, T., Çiçek, Ö., Ogar, P., Bürgi, M., Shaidani, N.I., Kaminski, M.M., Xu, Y., Grand, K., Vujanovic, M., Prata, D., Hildebrandt, F., Brox, T., Ronneberger, O., Voigt, F.F., Helmchen, F., Loffing, J., Horb, M.E., Willsey, H.R. and Lienkamp, S.S.
Abstract:Genome editing simplifies the generation of new animal models for congenital disorders. However, the detailed and unbiased phenotypic assessment of altered embryonic development remains a challenge. Here, we explore how deep learning (U-Net) can automate segmentation tasks in various imaging modalities, and we quantify phenotypes of altered renal, neural and craniofacial development in Xenopus embryos in comparison with normal variability. We demonstrate the utility of this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). We highlight how in toto light-sheet microscopy facilitates accurate reconstruction of brain and craniofacial structures within X. tropicalis embryos upon dyrk1a and six1 loss of function or treatment with retinoic acid inhibitors. These tools increase the sensitivity and throughput of evaluating developmental malformations caused by chemical or genetic disruption. Furthermore, we provide a library of pre-trained networks and detailed instructions for applying deep learning to the reader's own datasets. We demonstrate the versatility, precision and scalability of deep neural network phenotyping on embryonic disease models. By combining light-sheet microscopy and deep learning, we provide a framework for higher-throughput characterization of embryonic model organisms. This article has an associated 'The people behind the papers' interview.
Keywords:U-Net, Light-Sheet Microscopy, Deep Learning, Cystic Kidney Disease, Craniofacial Dysmorphia, Animals, Xenopus, Xenopus tropicalis, Xenopus laevis
Source:Development
ISSN:0950-1991
Publisher:Company of Biologists
Volume:148
Number:21
Page Range:dev199664
Date:1 November 2021
Official Publication:https://doi.org/10.1242/dev.199664
PubMed:View item in PubMed

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