Automated Brain Region Segmentation for Single Cell Resolution Histological Images Based on Markov Random Field

  • Xiaofeng Xu
  • Yue GuanEmail author
  • Hui Gong
  • Zhao Feng
  • Wenjuan Shi
  • Anan Li
  • Miao Ren
  • Jing Yuan
  • Qingming Luo
Original Article


The brain consists of massive regions with different functions and the precise delineation of brain region boundaries is important for brain region identification and atlas illustration. In this paper we propose a hierarchical Markov random field (MRF) model for brain region segmentation, where a MRF is applied to the downsampled low-resolution images and the result is used to initialize another MRF for the original high-resolution images. A fractional differential feature and a gray level co-occurrence matrix are extracted as the observed vector for the MRF and a new potential energy function, which can capture the spatial characteristic of brain regions, is proposed as well. A fuzzy entropy criterion is used to fine-tune the boundary from the hierarchical MRF model. We test the model both on synthetic images and real histological mouse brain images. The result suggests that the model can accurately identify target regions and even the whole mouse brain outline as a special case. An interesting observation is that the model cannot only segment regions with different cell density but also can segment regions with similar cell density and different cell morphology texture. Thus this model shows great potential for building the high-resolution 3D brain atlas.


Automated segmentation Brain atlas Markov random field 



This research is supported by the 973 projection (Grant No.2015CB755602), Science Fund for Creative Research Group of China (Grant No.61721092) and National Natural Science Foundation of China (Grant No. 91749209). We appreciate Shangbin Chen, Chaozhen Tan and Hong Ning for constructive suggestions, Wu Chen and Zhenyu Pan for image analysis.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for Optoelectronics, Huazhong University of Science and TechnologyWuhanChina
  2. 2.MoE Key Laboratory for Biomedical Photonics, School of Engineering SciencesHuazhong University of Science and TechnologyWuhanChina
  3. 3.HUST-Suzhou Institute for BrainsmaticsSuzhouChina

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