Collaborative Project

3D Tissue Reconstruction and Segmentation in Support of CCF Design

This project will expand the resolution of a successful mapping system for relatively large-scale organ features to the microscopic level. The HuBMAP CCF Object Library currently contains a three-dimensional map of structures within human organs that allow the location of tissue images to be mapped in a relatively coarse way. In this effort, Indiana University’s Mapping Component (MC) and GE Research’s Rapid Technology Implementation (RTI) group will develop computing tools to automatically (or with minimal human input) add small-scale functional tissue units (FTUs) and cell types to the CCR Object Library’s mapping system.

The effort will begin with a testbed based on data from human skin tissues, incorporating protein and structural landmarks for skin cell structures, immune cells and nerve cells residing in the skin, signs of UV damage and aging. The new set of waypoints will allow scientists to identify/register the location of a given research sample down to the level of individual cells and analyze spatial proximity of different cell types to each other and blood vessels. The result will be an expansion of the CCF Object Library toolset and documentation to provide Tissue Mapping Centers, Transformative Technology Development sites, and other projects within HuBMAP access to state-of-the-art 3D tissue reconstruction and segmentation algorithms and expertise.

Project leads
Katy Borner, Indiana University HIVE-MC
Learn more about Indiana University HIVE-MC.
Fiona Ginty, GE RTI
Learn more about GE RTI.


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