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Cell segmentation and tracking in phase contrast images using graph cut with asymmetric boundary costs

IEEE International Symposium on Biomedical Imaging (ISBI): 1220--1223, 2015
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Abstract: We propose a new robust, effective, and surprisingly simple approach for the segmentation of cells in phase contrast microscopy images. The key feature of our algorithm is that it strongly favors dark-to-bright transitions at the boundaries of the (arbitrarily shaped) segmentation mask. The segmentation mask can be effectively found by a fast min-cut approach. The small but essential difference to standard min-cut based approaches is that our graph contains directed edges with asymmetric edge weights. Combined with a simple region propagation our approach yields better segmentation results on the ISBI Cell Tracking Challenge 2014 dataset than the top ranked methods. We provide an easy-to-use open-source implementation for ImageJ/Fiji and Matlab on our homepage.

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See also

  • Slides (oral presentation at ISBI 2015, April 16-19, Brooklyn, NY, USA):
  • Slides (presentation at ISBI 2015, Cell Tracking Challenge (3rd Edition), April 16-19, Brooklyn, NY, USA):

BibTex references

@InProceedings{BR15,
  author       = "R.Bensch and O.Ronneberger",
  title        = "Cell segmentation and tracking in phase contrast images using graph cut with asymmetric boundary costs",
  booktitle    = "IEEE International Symposium on Biomedical Imaging (ISBI)",
  pages        = "1220--1223",
  year         = "2015",
  keywords     = "cell segmentation, cell tracking, phase contrast microscopy, graph-cut, min-cut, asymmetric boundary costs",
  url          = "http://lmb.informatik.uni-freiburg.de//Publications/2015/BR15"
}

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