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. 2018 May 16;8:7712. doi: 10.1038/s41598-018-26086-0

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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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Workflow of microCT guided sectioning. (A) Lungs were dissected from FVB mice. (B) Specimens were PTA stained, dehydrated and embedded either in paraffin or resin. (C) A microCT scan of each sample was performed and the position of interest defined within the 3D reconstructed phase retrieved data sets. (D) The samples were cut at the predefined ROI using either a standard microtome (paraffin) or cutting by grinding in combination with the laser microtome (resin) (left, TissueSurgeon, LLS ROWIAK LaserLabSolutions, image use permitted by LLS ROWIAK LaserLabSolutions under the Creative Commons Attribution License CC BY 4.0). (E) and (F) A virtual slice and a microscope image of the PTA stained lung tissue slices were produced and (G) the “degree of matching” was analysed using the developed block matching approach.