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PathoCellBench: A comprehensive benchmark for cell phenotyping

Item Type:Conference or Workshop Item
Title:PathoCellBench: A comprehensive benchmark for cell phenotyping
Creators Name:Lüscher, Jérôme, Koreuber, Nora, Franzen, Jannik, Reith, Fabian H., Winklmayr, Claudia, Baumann, Elias, Schürch, Christian M., Kainmüller, Dagmar and Rumberger, Josef Lorenz
Abstract:Digital pathology has seen the advent of a wealth of foundational models (FMs), yet to date their performance on cell phenotyping has not been benchmarked in a unified manner. We therefore propose PathoCellBench: A comprehensive benchmark for cell phenotyping on Hematoxylin and Eosin (H&E) stained histopathology images. We provide both PathoCell, a new H&E dataset featuring 14 cell types identified via multiplexed imaging, and ready-to-use fine-tuning and benchmarking code that allows the systematic evaluation of multiple prominent pathology FMs in terms of dense cell phenotype predictions in a range of generalization scenarios. We perform extensive benchmarking of existing FMs, providing insights into their generalization behavior under technical vs. medical domain shifts. Furthermore, while FMs achieve macro F1 scores > 0.70 on previously established benchmarks such as Lizard and PanNuke, on PathoCell, we observe scores as low as 0.20. This indicates a much more challenging task not captured by previous benchmarks, establishing PathoCell as a prime asset for future benchmarking of FMs and supervised models alike. Code and data are available on GitHub.
Keywords:Digital Pathology, Cell Phenotyping, Foundation Models
Source:Lecture Notes in Computer Science
Series Name:Lecture Notes in Computer Science (LNCS)
Title of Book:Medical Image Computing and Computer Assisted Intervention - MICCAI 2025
ISSN:0302-9743
ISBN:978-3-032-04980-3
Publisher:Springer
Volume:15966
Page Range:411-420
Number of Pages:10
Date:20 September 2025
Official Publication:https://doi.org/10.1007/978-3-032-04981-0_39
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