Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches

Tahsin Kurc, Spyridon Bakas, Xuhua Ren, Aditya Bagari, Alexandre Momeni, Yue Huang, Lichi Zhang, Ashish Kumar, Marc Thibault, Qi Qi, Qian Wang, Avinash Kori, Olivier Gevaert, Yunlong Zhang, Dinggang Shen, Mahendra Khened, Xinghao Ding, Ganapathy Krishnamurthi, Jayashree Kalpathy-Cramer, James DavisTianhao Zhao, Rajarsi Gupta, Joel Saltz, Keyvan Farahani

Research output: Contribution to journalArticlepeer-review

42 Citations (Scopus)


Biomedical imaging Is an important source of information in cancer research. Characterizations of cancer morphology at onset, progression, and in response to treatment provide complementary information to that gleaned from genomics and clinical data. Accurate extraction and classification of both visual and latent image features Is an increasingly complex challenge due to the increased complexity and resolution of biomedical image data. In this paper, we present four deep learning-based image analysis methods from the Computational Precision Medicine (CPM) satellite event of the 21st International Medical Image Computing and Computer Assisted Intervention (MICCAI 2018) conference. One method Is a segmentation method designed to segment nuclei in whole slide tissue images (WSIs) of adult diffuse glioma cases. It achieved a Dice similarity coefficient of 0.868 with the CPM challenge datasets. Three methods are classification methods developed to categorize adult diffuse glioma cases into oligodendroglioma and astrocytoma classes using radiographic and histologic image data. These methods achieved accuracy values of 0.75, 0.80, and 0.90, measured as the ratio of the number of correct classifications to the number of total cases, with the challenge datasets. The evaluations of the four methods indicate that (1) carefully constructed deep learning algorithms are able to produce high accuracy in the analysis of biomedical image data and (2) the combination of radiographic with histologic image information improves classification performance.

Original languageEnglish
Article number27
JournalFrontiers in Neuroscience
Publication statusPublished - 2020 Feb 21


  • classification
  • deep learning
  • digital pathology
  • image analysis
  • radiology
  • segmentation

ASJC Scopus subject areas

  • Neuroscience(all)


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