Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features
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Published:2021-05-17
Issue:2
Volume:26
Page:101-112
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ISSN:1083-3021
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Container-title:Journal of Mammary Gland Biology and Neoplasia
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language:en
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Short-container-title:J Mammary Gland Biol Neoplasia
Author:
Juppet Quentin,De Martino Fabio,Marcandalli Elodie,Weigert Martin,Burri Olivier,Unser Michael,Brisken Cathrin,Sage Daniel
Abstract
AbstractPatient-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 cell 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- and DAPI-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.
Funder
EPFL Open Science Fund and Swiss Data Science Center Swiss National Science Foundation CARIGEST SA EPFL Lausanne
Publisher
Springer Science and Business Media LLC
Subject
Cancer Research,Oncology
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