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

arXiv: https://arxiv.org/abs/2310.03106 · HTML: https://mlsanity.com/paper/2310.03106/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 39 references that are in the map.
- First posted on arXiv 4 Oct 2023.

## Builds on (most cited first, 13 of 13)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [VT-ADL: A Vision Transformer Network for Image Anomaly Detection and Localization](https://mlsanity.com/paper/2104.10036/) (2021)
- [Inpainting Transformer for Anomaly Detection](https://mlsanity.com/paper/2104.13897/) (2021)
- [Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides](https://mlsanity.com/paper/2101.07903/) (2021)
- [Deep Learning for Whole Slide Image Analysis: An Overview](https://mlsanity.com/paper/1910.11097/) (2019)
- [Yottixel -- An Image Search Engine for Large Archives of Histopathology Whole Slide Images](https://mlsanity.com/paper/1911.08748/) (2019)
- [One-Class Classification: A Survey](https://mlsanity.com/paper/2101.03064/) (2021)
- [AnoViT: Unsupervised Anomaly Detection and Localization with Vision Transformer-based Encoder-Decoder](https://mlsanity.com/paper/2203.10808/) (2022)
- [Pan-Cancer Diagnostic Consensus Through Searching Archival Histopathology Images Using Artificial Intelligence](https://mlsanity.com/paper/1911.08736/) (2019)
- [Learning Binary and Sparse Permutation-Invariant Representations for Fast and Memory Efficient Whole Slide Image Search](https://mlsanity.com/paper/2208.13653/) (2022)
- [Comments on 'Fast and scalable search of whole-slide images via self-supervised deep learning'](https://mlsanity.com/paper/2304.08297/) (2023)
- [A Preliminary Investigation into Search and Matching for Tumour Discrimination in WHO Breast Taxonomy Using Deep Networks](https://mlsanity.com/paper/2308.11162/) (2023)

## Built on by (most cited first, 4 of 4)

- [SPLICE -- Streamlining Digital Pathology Image Processing](https://mlsanity.com/paper/2404.17704/) (2024)
- [EvoPS: Evolutionary Patch Selection for Whole Slide Image Analysis in Computational Pathology](https://mlsanity.com/paper/2511.07560/) (2025)
- [Multi-Beholder: Biomarker Prediction for Low-Grade Glioma with Multiple Instance Learning and One-Class Classification](https://mlsanity.com/paper/2310.07464/) (2023)
- [A deep learning pipeline for PAM50 subtype classification using histopathology images and multi-objective patch selection](https://mlsanity.com/paper/2604.01798/) (2026)

## Abstract (arXiv)

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.