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. 2019 Jan 24;9:521. doi: 10.1038/s41598-018-36741-1

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© The Author(s) 2019

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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Segmentation of upper back part of mouse skin from Fig. 3b perfused with MHI148-PEI and clear with ECi using simple image processing pipeline: background removal using median filter and segmentation using Otsu thresholding in combination with binary morphological. On left: raw 3D data from small section of skin from upper back part. On right: segmentation using medial filter, thresholding and morphological filters.