2009 Winter Project Week Gofigure LevelSet

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Key Investigators

  • Kishore Mosaliganti, Harvard Medical School
  • Arnaud Gelas, Harvard Medical School
  • Alexandre Gouaillard, Harvard Medical School


  • Implement a 3D+t image analysis pipeline for multistain microscopy images
  • Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
  • Make a submission to Insight Journal

Approach, Plan

  • First prototype of filters are already implemented
  • Code review to be done with an ITK expert (luis/bill/jim?)
  • Run on cell datasets and build relevant tests
  • Write IJ paper
  • Submit



  1. Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
  2. Tensor Classification of N-point Correlation Function features for Histology Tissue Segmentation. K. Mosaliganti, F. Janoos, O. Irfanoglu, R. Ridgway, R. Machiraju, K. Huang, J. Saltz, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
  3. Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.