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. 2021 Feb 17;11:3981. doi: 10.1038/s41598-021-83264-3

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© The Author(s) 2021

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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A summary of histomorphometric procedures for estimating densities of Haversian canals and abnormal intra-cortical bone porosity. (a, b): localised histology (60 ×) viewed under linearly polarised light showing secondary osteon lamellae (white arrows) surrounding Haversian canals (oval features), which were obscured by patches of diagenesis (grey arrows). Cement lines (black arrow in b) were inconsistently preserved (examples shown are from individuals BG2 (a) and Sk9.3 (b). Haversian canals were counted manually form thresholded images (c–f): (c) shows numbered canals, (d) shows manual segmentation of cortical wall from abnormal intra-cortical porosity (red dashed line), while the solid line marks whole section area in individual BG2; (e) illustrates final counts of Haversian canals, while (f) shows ‘extracted’ abnormal bone porosity.