From slides to AI-ready maps: Standardized multi-layer tissue maps as metadata for artificial intelligence in digital pathology

TL;DR

This paper introduces a standardized framework for creating multi-layer tissue maps from Whole Slide Images, enabling better metadata management and improved AI training and research in digital pathology.

Contribution

It proposes a novel, interoperable method to generate structured tissue maps with three layers, enhancing metadata consistency and AI application in pathology.

Findings

Generated tissue maps improve searchability in WSI archives

Standardized metadata facilitates AI training and validation

Enhanced dataset quality for cancer research

Abstract

A Whole Slide Image (WSI) is a high-resolution digital image created by scanning an entire glass slide containing a biological specimen, such as tissue sections or cell samples, at multiple magnifications. These images are digitally viewable, analyzable, and shareable, and are widely used for Artificial Intelligence (AI) algorithm development. WSIs play an important role in pathology for disease diagnosis and oncology for cancer research, but are also applied in neurology, veterinary medicine, hematology, microbiology, dermatology, pharmacology, toxicology, immunology, and forensic science. When assembling cohorts for AI training or validation, it is essential to know the content of a WSI. However, no standard currently exists for this metadata, and such a selection has largely relied on manual inspection, which is not suitable for large collections with millions of objects. We propose a general framework to generate 2D index maps (tissue maps) that describe the morphological content of WSIs using common syntax and semantics to achieve interoperability between catalogs. The tissue maps are structured in three layers: source, tissue type, and pathological alterations. Each layer assigns WSI segments to specific classes, providing AI-ready metadata. We demonstrate the advantages of this standard by applying AI-based metadata extraction from WSIs to generate tissue maps and integrating them into a WSI archive. This integration enhances search capabilities within WSI archives, thereby facilitating the accelerated assembly of high-quality, balanced, and more targeted datasets for AI training, validation, and cancer research.