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. 2017 Nov 1;13:76. doi: 10.1186/s13007-017-0229-8

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© The Author(s) 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 3 — Image segmentation. a µCT cross section image of a typical spike in 16-bit greyscale, b initial thresholding using our adaptive method, c erosion to remove outlying objects using a disk structuring element (SE), d median filter applied to smooth and further segment region of interest (ROI), e image dilated by same SE as (c) and with remaining holder removed and f final result of this process was obtained by using (e) as a mask in conjunction with (a)