Bilkent University
Department of Computer Engineering


Deep Learning Based Unsupervised Tissue Segmentation in Histopathological Images


Troya Çağıl Köylü
MS Student
(Supervisor: Doç. Dr. Çiğdem Gündüz Demir )
Computer Engineering Department
Bilkent University

In the current practice of medicine, histopathological examination of tissues is essential for cancer diagnosis. However, this task is both subject to observer variability and time consuming for pathologists. Thus, it is important to develop automated objective tools, the first step of which usually comprises image segmentation. According to this need, in this thesis, we propose a novel approach for the segmentation of histopathological tissue images. Our proposed method called deepSeg is a two-tier method. The first tier transfers the knowledge from AlexNet, which is a convolutional neural network (CNN) trained for the non-medical domain of ImageNet, to the medical domain of histopathological tissue image characterization. The second tier uses this characterization in a seed-based region growing algorithm, for the unsupervised segmentation of heterogeneous tissue images into their homogeneous regions. To test the effectiveness of the segmentation, we conduct experiments on microscopic colon tissue images. Quantitative results reveal that the proposed method improves the performance of the previous methods that work on the same dataset. This study both illustrates one of the first successful demonstrations of using deep learning for tissue image segmentation, and shows the power of using deep learning features instead of handcrafted ones in the domain of histopathological image analysis.


DATE: 02 November 2017, Thursday @ 13:40