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Ascidian Cells

Segmentation of ascidian notochord cells in DIC timelapse images

We have developed a method to automatically segment notochord cell boundaries from differential interference contrast (DIC) timelapse images of the elongating ascidian tail. The method is based on a specialized parametric active contour, the network snake, which can be initialized as a network of arbitrary but fixed topology and provides an effective framework for simultaneously segmenting multiple touching cells. Several modifications to the original network snake were necessary for high-quality segmentation, including linear Gaussian derivative filtering to reconstruct edge maps from DIC images and a new energy function to improve the segmentation of critical cell-cell vertices.

Network snake approach for segmentation of ascidian notochord cells in DIC timelapse images.

Network snake approach for segmentation of ascidian notochord cells in DIC timelapse images.

Collaborators:

  • Prof. B.S. Manjunanth, Bio-Informatics Lab and Vision Research Lab, University of California, Santa Barbara, USA

Publications:

  • [2011,article] bibtex
    B. Obara, M. Veeman, J. H. Choi, W. Smith, and B. S. Manjunath, "Segmentation of ascidian notochord cells in DIC timelapse images," Microscopy Research and Technique, vol. 74, iss. 8, pp. 727-734, 2011.
    @article{Obara2010d,
      author = {Boguslaw Obara and Michael Veeman and Jae Hyeok Choi and William Smith and B. S. Manjunath},
      title = {Segmentation of ascidian notochord cells in {DIC} timelapse images},
      journal = {Microscopy Research and Technique},
      volume = {74},
      number = {8},
      pages = {727-734},
      year = {2011}
    }