Creating an Atlas of Normal Tissue for Pruning WSI Patching Through Anomaly Detection

Peyman Nejat; Areej Alsaafin; Ghazal Alabtah; Nneka Comfere; Aaron Mangold; Dennis Murphree; Patricija Zot; Saba Yasir; Joaquin J. Garcia; H. R. Tizhoosh

arXiv · 2310.03106

Creating an Atlas of Normal Tissue for Pruning WSI Patching Through Anomaly Detection

Peyman Nejat·Areej Alsaafin·Ghazal Alabtah·Nneka Comfere·Aaron Mangold·Dennis Murphree·Patricija Zot·Saba Yasir·Joaquin J. Garcia·H. R. Tizhoosh

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Abstract

Patching gigapixel whole slide images (WSIs) is an important task in computational pathology. Some methods have been proposed to select a subset of patches as WSI representation for downstream tasks. While most of the computational pathology tasks are designed to classify or detect the presence of pathological lesions in each WSI, the confounding role and redundant nature of normal histology in tissue samples are generally overlooked in WSI representations. In this paper, we propose and validate the concept of an "atlas of normal tissue" solely using samples of WSIs obtained from normal tissue biopsies. Such atlases can be employed to eliminate normal fragments of tissue samples and hence increase the representativeness collection of patches. We tested our proposed method by establishing a normal atlas using 107 normal skin WSIs and demonstrated how established indexes and search engines like Yottixel can be improved. We used 553 WSIs of cutaneous squamous cell carcinoma (cSCC) to show the advantage. We also validated our method applied to an external dataset of 451 breast WSIs. The number of selected WSI patches was reduced by 30% to 50% after utilizing the proposed normal atlas while maintaining the same indexing and search performance in leave-one-patinet-out validation for both datasets. We show that the proposed normal atlas shows promise for unsupervised selection of the most representative patches of the abnormal/malignant WSI lesions.

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Peyman Nejat, Areej Alsaafin, Ghazal Alabtah, Nneka Comfere, Aaron Mangold, Dennis Murphree, Patricija Zot, Saba Yasir, Joaquin J. Garcia, H. R. Tizhoosh. 2023-10-04. Creating an Atlas of Normal Tissue for Pruning WSI Patching Through Anomaly Detection. https://arxiv.org/abs/2310.03106

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