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Front. Med. | doi: 10.3389/fmed.2019.00173

Multi-organ gland segmentation using deep learning

Thomas Binder1,  El Mehdi Tantaoui1, Pushpak Pati2,  Raúl Catena2,  Ago Set-Aghayan1 and Maria Gabrani2*
  • 1IBM (France), France
  • 2IBM Research - Zurich, Switzerland

Clinical morphological analysis of histopathology samples is an effective method in cancer diagnosis. Computational pathology methods can be employed to automate this analysis, providing improved objectivity and scalability. More specifically, computational techniques can be used in segmenting glands, which is an essential factor in cancer diagnosis. Automatic delineation of glands is a challenging task considering a large variability in glandular morphology across tissues and pathological subtypes. A deep learning based gland segmentation method can be developed to address the above task, but it requires a large number of accurate gland annotations from several tissue slides. Such a large dataset need to be generated manually by experienced pathologists, which is laborious, time-consuming, expensive and suffers from the subjectivity of the annotator. So far, deep learning techniques have produced promising results on a few organ-specific gland segmentation tasks, however, the demand for organ-specific gland annotations hinder the extensibility of these techniques to other organs. This work investigates the idea of cross-domain (-organ type) approximation that aims at reducing the need for organ-specific annotations. Unlike parenchyma, the stromal component of tissues, that lies between the glands, is more consistent across several organs. It is hypothesized that an automatic method, that can precisely segment the stroma, would pave the way for a cross-organ gland segmentation. Two proposed Dense-U-Nets are trained on hematoxylin and eosin (H&E) stained colon adenocarcinoma samples focusing on the gland and stroma segmentation. The trained networks are evaluated on two independent datasets, they are, a H&E stained colon adenocarcinoma dataset and a H&E stained breast invasive cancer dataset. The trained network targeting the stroma segmentation performs similar to the network targeting the gland segmentation on the colon dataset. Whereas, the former approach performs significantly better compared to the latter approach on the breast dataset, showcasing the higher generalization capacity of the stroma segmentation approach. The networks are evaluated using Dice coefficient and Hausdorff distance computed between the ground truth gland masks and the predicted gland masks. The conducted experiments validate the efficacy of the proposed stoma segmentation approach towards multi-organ gland segmentation.

Keywords: Stroma, deep learning, digital pathology, Gland detection, WSI

Received: 05 May 2019; Accepted: 12 Jul 2019.

Edited by:

Behzad Bozorgtabar, École Polytechnique Fédérale de Lausanne, Switzerland

Reviewed by:

Jan Egger, Graz University of Technology, Austria
Shiba Kuanar, The University of Iowa, United States  

Copyright: © 2019 Binder, Tantaoui, Pati, Catena, Set-Aghayan and Gabrani. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Maria Gabrani, IBM Research - Zurich, Rüschlikon, 8803, Switzerland,