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. 2018 Nov 8;8:16531. doi: 10.1038/s41598-018-34848-z

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Pipeline for quantitative 3D morphometric analysis After breeding and fish husbandry, the specimens are fixed and stained with contrast agent. 3D data sets are acquired with X-ray micro-CT at the synchrotron radiation facility. Manual segmentation leads to a reference atlas. Each new dataset is rescaled and aligned with respect to the reference model. For each organ of interest the subvolume is extracted. The atlas labels for the organ of interest are then registered and deformed to create new automatically segmented labels.