Jim Denholm

B. A. Schreiber, J. Denholm, F. Jaeckle et al.

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.

Yanqi Cheng, Chun-Wun Cheng, Jim Denholm et al.

Medical imaging pipelines critically rely on robust denoising to stabilise downstream tasks such as segmentation and reconstruction. However, many existing denoisers depend on large annotated datasets or supervised learning, which restricts their usability in clinical environments with heterogeneous modalities and limited ground-truth data. To address this limitation, we introduce DNA-Prior, a universal unsupervised denoising framework that reconstructs clean images directly from corrupted observations through a mathematically principled hybrid prior. DNA-Prior integrates (i) an implicit architectural prior, enforced through a deep network parameterisation, with (ii) an explicit spectral-spatial prior composed of a frequency-domain fidelity term and a spatial regularisation functional. This dual-domain formulation yields a well-structured optimisation problem that jointly preserves global frequency characteristics and local anatomical structure, without requiring any external training data or modality-specific tuning. Experiments across multiple modalities show that DNA achieves consistent noise suppression and structural preservation under diverse noise conditions.