Automatic extraction of cell nuclei from H&E-stained histopathological images

Faliu Yi, Junzhou Huang, Lin Yang, Yang Xie, Guanghua Xiao

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


Extraction of cell nuclei from hematoxylin and eosin (H&E)-stained histopathological images is an essential preprocessing step in computerized image analysis for disease detection, diagnosis, and prognosis. We present an automated cell nuclei segmentation approach that works with H&E-stained images. A color deconvolution algorithm was first applied to the image to get the hematoxylin channel. Using a morphological operation and thresholding technique on the hematoxylin channel image, candidate target nuclei and background regions were detected, which were then used as markers for a marker-controlled watershed transform segmentation algorithm. Moreover, postprocessing was conducted to split the touching nuclei. For each segmented region from the previous steps, the regional maximum value positions were identified as potential nuclei centers. These maximum values were further grouped into k-clusters, and the locations within each cluster were connected with the minimum spanning tree technique. Then, these connected positions were utilized as new markers for a watershed segmentation approach. The final number of nuclei at each region was determined by minimizing an objective function that iterated all of the possible k-values. The proposed method was applied to the pathological images of the tumor tissues from The Cancer Genome Atlas study. Experimental results show that the proposed method can lead to promising results in terms of segmentation accuracy and separation of touching nuclei.

Original languageEnglish (US)
Article number027502
JournalJournal of Medical Imaging
Issue number2
StatePublished - Apr 1 2017


  • cell nuclei extraction
  • color deconvolution
  • digital pathology
  • hematoxylin and eosin-stained image
  • image analysis
  • watershed transform

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging


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