Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features

Patient-Derived Xenografts (PDXs) are the preclinical models which best recapitulate inter- and intra-patient complexity of human breast malignancies, and are also emerging as useful tools to study the normal breast epithelium. However, data analysis generated with such models is often confounded by the presence of host cells and can give rise to data misinterpretation. For instance, it is important to discriminate between xenografted and host cells in histological sections prior to performing immunostainings. We developed Single Cell Classifier (SCC), a data-driven deep learning-based computational tool that provides an innovative approach for automated cell species discrimination based on a multi-step process entailing nuclei segmentation and single cell classification. We show that human and murine cells contextual features, more than cell-intrinsic ones, can be exploited to discriminate between cell species in both normal and malignant tissues, yielding up to 96% classification accuracy. SCC will facilitate the interpretation of H&E stained histological sections of xenografted human-in-mouse tissues and it is open to new in-house built models for further applications. SCC is released as an open-source plugin in ImageJ/Fiji available at the following link: https://github.com/Biomedical-Imaging-Group/SingleCellClassifier. Author summaryBreast cancer is the most commonly diagnosed tumor in women worldwide and its incidence in the population is increasing over time. Because our understanding of such disease has been hampered by the lack of adequate human preclinical model, efforts have been made in order to develop better approaches to model the human complexity. Recent advances in this regard were achieved with Patient-Derived Xenografts (PDXs), which entail the implantation of human-derived specimens to recipient immunosuppressed mice and are, thus far, the preclinical system best recapitulating the heterogeneity of both normal and malignant human tissues. However, histological analyses of the resulting tissues are usually confounded by the presence of cells of different species. To circumvent this hurdle and to facilitate the discrimination of human and murine cells in xenografted samples, we developed Single Cell Classifier (SCC), a deep learning-based open-source software, available as a plugin in ImageJ/Fiji, performing automated species classification of individual cells in H&E stained sections. We show that SCC can reach up to 96% classification accuracy to classify cells of different species mainly leveraging on their contextual features in both normal and tumor PDXs. SCC will improve and automate histological analyses of human-in-mouse xenografts and is open to new in-house built models for further classification tasks and applications in image analysis.