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. 2018 Dec 18;5:180294. doi: 10.1038/sdata.2018.294

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Copyright © 2018, The Author(s)

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/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article.

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(a–d) A μCT-based 3D whole body organ segmentation of a mouse is performed semi-automatically for bones (beige), lung (pink), and spleen (dark green). Other organs are segmented by manual delineation: liver (brown), stomach (light tan), kidneys (yellow), intestine (light green, only depicted in d), tumor (orange), part of the thigh muscle (blue), and bladder (gold). For the segmentation process, organs need to be encircled in several slices such as (b) coronal and (c) axial from which a program can interpolate the remaining slices. (d) Example of the manual delineation procedure by drawing scribbles (green line) around the right kidney. Mouse #M03-004h of the contrast-enhanced dataset was used in this example.