CellPath-Bench: A Multidimensional Benchmark for Whole-Slide Cellular Representations in Pathology Foundation Models

TL;DR - CellPath-Bench is a cellular-resolution benchmark for evaluating how well frozen pathology foundation models encode cell-type information in whole-slide images. It enables standardized comparison of both within-section decodability and transfer across tissue sections, datasets, and organs.

• Uses 25 spatially aligned H&E–Xenium tissue sections spanning 11 organs and more than 7 million cells.
• Samples frozen whole-slide feature maps at registered nuclear coordinates and evaluates them with standardized multiclass linear probes.
• Introduces Cell Representation Advantage for comparing nucleus-anchored features with patch-level pooling, and Cell Representation Transferability for measuring cross-domain generalization.
• Evaluates 30 pathology-specific and general-purpose foundation models across 304,920 runs, revealing distinct model-dependent capability profiles.