Aignostics Launches Atlas H&E-TME for Scalable Tumor Microenvironment Analysis from Routine Pathology Slides

Following early access pilots with leading biopharma partners, Aignostics has officially launched Atlas H&E-TME, a new AI-powered application designed to analyze the tumor microenvironment (TME) directly from routine H&E-stained pathology slides. The solution offers a scalable, cost-effective alternative to traditional methods that rely on multiplex staining or specialized imaging, helping researchers extract rich insights from standard diagnostic workflows.

Built on the Atlas foundation model, which was co-developed by Aignostics, Mayo Clinic, and Charité Berlin, Atlas H&E-TME analyzes whole-slide images within hours—providing detailed readouts of seven tissue types, nine immune cell classes, and over 5,000 quantitative metrics per image. The application aims to accelerate cancer research by enabling high-throughput, high-resolution profiling of immune landscapes, spatial relationships, and tissue architecture across a range of cancer types.

"This is the first time I have seen a model that demonstrates consistently high accuracy across multiple cancer indications with exceptional robustness," said Dr. Frederick Klauschen, Co-Founder of Aignostics and Director of the Institute of Pathology at Ludwig-Maximilians-Universität München.

“Understanding the TME is essential for developing effective cancer therapies, but traditional approaches are costly, time-consuming, and often limited in scale,” added Viktor Matyas, Co-Founder and CEO of Aignostics. “Atlas H&E-TME changes this paradigm. Our pilots with biopharma have confirmed we can deliver high-quality results with unparalleled accuracy, speed, and scale, helping researchers get maximum value from every H&E image.”

Atlas H&E-TME is available as a self-service application, with upcoming integrations planned for major digital pathology and image management systems. It has been extensively validated on primary and metastatic samples from a wide variety of labs and scanners to ensure robustness and generalizability in real-world conditions. Validation metrics are available to new partners upon request.

The application supports a wide range of research workflows, including:

• Rapid identification and characterization of tumors with immune infiltration

• Quantification of immune cell populations and tissue features

• Integration of H&E data with spatial transcriptomics for refined niche analysis

Initially, Atlas H&E-TME will be available to biopharma organizations studying breast, bladder, colorectal, liver, and lung cancers. Academic access and support for additional cancer types will roll out in the coming months.

With Atlas H&E-TME, Aignostics is aiming to democratize access to deep TME insights—offering a faster, scalable solution that brings advanced computational pathology into standard research pipelines.