# Atlas H&E-TME: Scalable AI-Based Tissue Profiling at Expert Pathologist-Level Accuracy

arXiv: https://arxiv.org/abs/2606.12346 · HTML: https://mlsanity.com/paper/2606.12346/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 44 references that are in the map.
- First posted on arXiv 10 Jun 2026.

## Builds on (most cited first, 19 of 19)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Selective Classification for Deep Neural Networks](https://mlsanity.com/paper/1705.08500/) (2017)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Cell Detection with Star-convex Polygons](https://mlsanity.com/paper/1806.03535/) (2018)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification](https://mlsanity.com/paper/2108.11195/) (2021)
- [RudolfV: A Foundation Model by Pathologists for Pathologists](https://mlsanity.com/paper/2401.04079/) (2024)
- [NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation](https://mlsanity.com/paper/2102.09099/) (2021)
- [Epithelium segmentation using deep learning in H&E-stained prostate specimens with immunohistochemistry as reference standard](https://mlsanity.com/paper/1808.05883/) (2018)
- [Multi-Class Cell Detection Using Spatial Context Representation](https://mlsanity.com/paper/2110.04886/) (2021)
- [CellViT++: Energy-Efficient and Adaptive Cell Segmentation and Classification Using Foundation Models](https://mlsanity.com/paper/2501.05269/) (2025)
- [Atlas: A Novel Pathology Foundation Model by Mayo Clinic, Charit'e, and Aignostics](https://mlsanity.com/paper/2501.05409/) (2025)
- [Atlas 2 -- Foundation models for clinical deployment](https://mlsanity.com/paper/2601.05148/) (2026)
- [Variability Matters : Evaluating inter-rater variability in histopathology for robust cell detection](https://mlsanity.com/paper/2210.05175/) (2022)
- [OpenTME: An Open Dataset of AI-powered H&E Tumor Microenvironment Profiles from TCGA](https://mlsanity.com/paper/2604.12075/) (2026)
- [PhenoBench: A Comprehensive Benchmark for Cell Phenotyping](https://mlsanity.com/paper/2507.03532/) (2025)

## Built on by (most cited first, 1 of 1)

- [LUCAID: Agentic Multimodal AI for Lung Cancer Precision Pathology](https://mlsanity.com/paper/2608.23803/) (2026)

## Abstract (arXiv)

Hematoxylin and eosin (H&E) staining is the cornerstone of histopathology, yet scalable, quantitative analysis of H&E whole-slide images (WSIs) remains a central challenge in computational pathology. We present Atlas H&E-TME, an AI-based system built on the Atlas family of pathology foundation models that predicts tissue quality, tissue region, and cell type labels across multiple cancer types, yielding over 4,500 quantitative readouts per slide at cell-level resolution. A key challenge to validating such systems is overcoming morphological ambiguity inherent to H&E-only ground truth and the limited scalability of more informed references drawing on modalities such as immunohistochemistry (IHC). We address this with a dual validation framework combining biologically grounded depth with technical and morphological breadth. For depth, we propose an IHC-informed multi-pathologist consensus protocol that substantially improves inter-rater agreement over conventional H&E-only annotation. This yields a molecularly grounded reference against which we compare Atlas H&E-TME and pathologists working from H&E alone. For breadth, we benchmark Atlas H&E-TME on over 200,000 high-confidence H&E-only pathologist annotations across 1,500+ cases spanning eight cancer types and their most common metastatic sites, with subtypes covering >90% of clinical cases per cancer type, drawn from 25+ sources and 8+ scanner models. Benchmarked against the IHC-informed consensus, Atlas H&E-TME matches or exceeds pathologist H&E-only performance and generalizes consistently and robustly across this broad morphological and technical scope. In doing so, Atlas H&E-TME turns the H&E slide -- the most ubiquitous data in pathology -- into a scalable, quantitative window into the tumor and its microenvironment, laying a foundation for the next generation of tissue-based biomarkers in translational and clinical research.