MiroSCOPE: An AI-driven digital pathology platform for annotating functional tissue units

Fenner, M. R.; Sevim, S.; Wu, G.; Beavers, D.; Guo, P.; Tang, Y.; Eddy, C. Z.; Ait-Ahmad, K.; Rice-Stitt, T.; Thomas, G.; Kuykendall, M. J.; Stavrinides, V.; Emberton, M.; Xu, D.; Song, X.; Eksi, S. E.; Demir, E.

doi:10.1101/2025.07.11.664228

bioRxiv · 10.1101/2025.07.11.664228

MiroSCOPE: An AI-driven digital pathology platform for annotating functional tissue units

Fenner, M. R.·Sevim, S.·Wu, G.·Beavers, D.·Guo, P.·Tang, Y.·Eddy, C. Z.·Ait-Ahmad, K.·Rice-Stitt, T.·Thomas, G.·Kuykendall, M. J.·Stavrinides, V.·Emberton, M.·Xu, D.·Song, X.·Eksi, S. E.·Demir, E.

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Abstract

Cancer tissue analysis in digital pathology is typically conducted across different spatial scales, ranging from high-resolution cell-level modeling to lower-resolution tile-based assessments. However, these perspectives often overlook the structural organization of functional tissue units (FTUs), the small, repeating structures which are crucial to tissue function and key factors during pathological assessment. The incorporation of FTU information is hindered by the need for detailed manual annotations, which are costly and time-consuming to obtain. While artificial intelligence (AI)-based solutions hold great promise to accelerate this process, there is currently no comprehensive workflow for building the large, annotated cohorts required. To remove these roadblocks and advance the development of more interpretable approaches, we developed MiroSCOPE, an end-to-end AI-assisted platform for annotating FTUs at scale, built on QuPath. MiroSCOPE integrates a fine-tunable multiclass segmentation model and curation-specific usability features to enable a human-in-the-loop system that accelerates AI annotation by a pathologist. The system is used to efficiently annotate over 71,900 FTUs on 184 prostate cancer hematoxylin and eosin (H&E)-stained tissue samples and demonstrates ready translation to breast cancer. Furthermore, we publicly release a dataset named Miro-120, consisting of 120 prostate cancer H&E with 30,568 annotations, which can be used by the community as a high-quality resource for FTU-level machine learning aims. In summary, MiroSCOPE provides an adaptable AI-driven platform for annotating functional tissue units, facilitating the use of structural information in digital pathology analyses.

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Fenner, M. R., Sevim, S., Wu, G., Beavers, D., Guo, P., Tang, Y., Eddy, C. Z., Ait-Ahmad, K., Rice-Stitt, T., Thomas, G., Kuykendall, M. J., Stavrinides, V., Emberton, M., Xu, D., Song, X., Eksi, S. E., Demir, E.. 2025-07-17. MiroSCOPE: An AI-driven digital pathology platform for annotating functional tissue units. https://doi.org/10.1101/2025.07.11.664228

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