# Rapid Artefact Removal and H&E-Stained Tissue Segmentation

arXiv: https://arxiv.org/abs/2308.13304 · HTML: https://mlsanity.com/paper/2308.13304/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 3 of its 14 references that are in the map.
- First posted on arXiv 25 Aug 2023.

## Builds on (most cited first, 3 of 3)

- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [Predicting breast tumor proliferation from whole-slide images: the TUPAC16 challenge](https://mlsanity.com/paper/1807.08284/) (2018)
- [A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis](https://mlsanity.com/paper/2001.00258/) (2020)

## Built on by (most cited first, 2 of 2)

- [Reliable Benchmarking of Artifact Detection in Computational Pathology: A Reproducibility and Uncertainty Analysis](https://mlsanity.com/paper/2608.30835/) (2026)
- [Mitigating Batch Effects in Histopathology via Language-Mediated Robust Embedding Generation](https://mlsanity.com/paper/2606.28697/) (2026)

## Abstract (arXiv)

We present an innovative method for rapidly segmenting hematoxylin and eosin (H&E)-stained tissue in whole-slide images (WSIs) that eliminates a wide range of undesirable artefacts such as pen marks and scanning artefacts. Our method involves taking a single-channel representation of a lowmagnification RGB overview of the WSI in which the pixel values are bimodally distributed such that H&E-stained tissue is easily distinguished from both background and a wide variety of artefacts. We demonstrate our method on 30 WSIs prepared from a wide range of institutions and WSI digital scanners, each containing substantial artefacts, and compare it to segmentations provided by Otsu thresholding and Histolab tissue segmentation and pen filtering tools. We found that our method segmented the tissue and fully removed all artefacts in 29 out of 30 WSIs, whereas Otsu thresholding failed to remove any artefacts, and the Histolab pen filtering tools only partially removed the pen marks. The beauty of our approach lies in its simplicity: manipulating RGB colour space and using Otsu thresholding allows for the segmentation of H&E-stained tissue and the rapid removal of artefacts without the need for machine learning or parameter tuning.