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bioRxiv · 10.1101/2025.08.26.672346

Histolytics: A Panoptic Spatial Analysis Framework for Interpretable Histopathology

Lehtonen, O.·Nordlund, N.·Salloum, S.·Kalliala, I.·Virtanen, A.·Hautaniemi, S.
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Abstract

Quantifying spatial organization in hematoxylin and eosin (H&E)-stained whole-slide images (WSIs) is essential for uncovering tissue-level patterns relevant to pathology. We present Histolytics, an open-source, scalable Python framework for interpretable, WSI-scale histopathological analysis. Histolytics integrates panoptic segmentation with spatial querying, morphological profiling, and graph-based analytics to enable high-resolution, quantitative characterization of nuclei, tissue compartments, and the extracellular matrix (ECM). Designed to align with diagnostic reasoning, Histolytics supports segmentation with state-of-the-art deep learning models and provides modular tools for extracting biologically grounded features across entire WSIs. By leveraging spatially contextualized measurements at cellular and tissue levels, Histolytics addresses a critical gap in explainable computational pathology, offering an interpretable alternative or complement to black-box predictive models. The framework is compatible with the broader Python data science ecosystem and includes extensive documentation and pretrained models to promote widespread adoption.

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Lehtonen, O., Nordlund, N., Salloum, S., Kalliala, I., Virtanen, A., Hautaniemi, S.. 2025-08-31. Histolytics: A Panoptic Spatial Analysis Framework for Interpretable Histopathology. https://doi.org/10.1101/2025.08.26.672346

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