The effects of despeckling filters on pore size measurements in collagen scaffold micro-CT data.
Journal of microscopy
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Meek, M., Best, S., & Cameron, R. (2021). The effects of despeckling filters on pore size measurements in collagen scaffold micro-CT data.. Journal of microscopy https://doi.org/10.1111/jmi.13050
Micro-CT is often used to assess the characteristics of porous structures such as tissue engineering scaffolds and trabecular bone. Prior to analysis micro-CT images can be thresholded and filtered to remove noise. Scaffold pore size affects mechanical properties and biological cell behaviour and is a frequently assessed parameter. This paper identifies and characterises an artefact affecting a commonly used filter which erroneously increases mean pore size. The 3D sweep despeckling filter removes all but the largest object within a volume of interest, and therefore deletes any disconnected objects located at the periphery, increasing measured mean pore size. This artefact is characterised, and effective methods to mitigate its effects are devised, involving despeckling a sufficiently large volume of interest, then reducing the volume of interest in size to remove the error prior to analysis. Techniques to effectively apply this method to other datasets are described. This method eliminates the artefact but is time consuming and computationally expensive. Alternative, more economical filters which remove objects below a specified size are also assessed but are shown to be affected by the same artefact. These results will help guide the implementation of future studies investigating the effects of pore size.
Department of Materials Science and Metallurgy, University of Cambridge and EPSRC Established Career Fellowship Grant No. EP/N019938/1
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External DOI: https://doi.org/10.1111/jmi.13050
This record's URL: https://www.repository.cam.ac.uk/handle/1810/325257
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