2009 Winter Project Week Tumor Microenvironment

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Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue.

Key Investigators

• The Ohio State University: Shantanu Singh, Raghu Machiraju
• GE Global Research: Jens Rittscher
• BWH: Michael Halle, Steve Pieper, Wendy Plesniak

Objective

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).

Approach, Plan

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework. Begin with level set methods of [Mosaliganti 2008] (middle image). Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results. Also, explore labeling capabilities of Slicer3.

Progress

Updated every day of Project Week.

References

• T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
• Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008