Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma

Recent advances in digital pathology have enabled comprehensive analyses of Whole-Slide Images (WSIs) from tissue samples, leveraging high-resolution microscopy and computational capabilities. Despite this progress, available tools for automatic cell type identification perform poorly on skin tissue, e.g. in the classification of non-melanoma tumor cells. This is due to a paucity of labeled training data sets and high morphological similarities between tumor and non-tumor epithelial cells in the skin. Here, we propose Histo-Miner, a deep learning-based pipeline designed for the analysis of skin WSIs. To this end we generated two new datasets using WSIs of cutaneous Squamous Cell Carcinoma (cSCC) samples, a frequent non-melanoma skin cancer, by annotating 47,392 cell nuclei across 5 cell types in 21 WSIs and segmenting tumor regions in 144 WSIs. Histo-Miner employs convolutional neural networks and vision transformers for nucleus segmentation and classification, as well as tumor region segmentation. Performance of trained models positively compares to state of the art with multi-class Panoptic Quality (mPQ) of 0.569 for nucleus segmentation, macro-averaged F1 of 0.832 for nucleus classification and mean Intersection over Union (mIoU) of 0.907 for tumor region segmentation. From these output, the pipeline can generate a compact feature vector summarizing tissue morphology and cellular interactions, which can be used for various downstream tasks. As an exemplary use-case, we deploy Histo-Miner to predict cSCC patient response to immunotherapy based on pre-treatment WSIs from 45 patients. Histo-Miner predicts patient response with mean area under ROC curve of 0.755 ± 0.091 over cross-validation, and identifies percentages of lymphocytes, the granulocyte to lymphocyte ratio in tumor vicinity and the distances between granulocytes and plasma cells in tumors as predictive features for therapy response. This highlights the applicability of Histo-Miner to clinically relevant scenarios, providing direct interpretation of the classification and insights into the underlying biology. Importantly, Histo-Miner is designed to allow for its use on other cancer types and on other training datasets. Our tool and datasets are available through our github repository: https://github.com/bozeklab/histo-miner.