Bang and the Artefacts are Gone! Rapid Artefact Removal and Tissue Segmentation in Haematoxylin and Eosin Stained Biopsies

08/25/2023
by   B. A. Schreiber, et al.
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We present H E Otsu thresholding, a scheme for rapidly detecting tissue in whole-slide images (WSIs) that eliminates a wide range of undesirable artefacts such as pen marks and scanning artefacts. Our method involves obtaining a bid-modal representation of a low-magnification RGB overview image which enables simple Otsu thresholding to separate tissue from background and artefacts. We demonstrate our method on WSIs prepared from a wide range of institutions and WSI digital scanners, each containing substantial artefacts that cause other methods to fail. The beauty of our approach lies in its simplicity: manipulating RGB colour space and using Otsu thresholding allows for the rapid removal of artefacts and segmentation of tissue.

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