ITK Release 4/A2D2 Projects/Confocal Microscopy

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A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies


There is a growing body of cancer biology research that relies heavily on 3D cellular model systems. In recent years, there has been especially much interest in the tumor microenvironment (TME) that surrounds epithelial tumors. Fluorescence markers and confocal and multi-photon microscopes are employed towards the creation of the required virtual 3D annotated models of the TME.


We propose to create a comprehensive ITKv4 application that includes

  • Tangible workflows for preprocessing images (denoising), and
  • Segmenting, classifying and visualizing cell nuclei and their arrangements.

Emphasis will be placed on creating tangible shape spaces and tools that will associate cellular (nuclei) phenotypes to regions in the microenvironment.

We will leverage our extensive experience in developing algorithms for processing confocal stacks from thick tissue sections. The proposed tool will facilitate the use of ITKv4 among an important and growing community of cancer researchers.


  • Raghu Machiraju (Ohio State University),
  • Kun Huang