View source for ITK Release 4/A2D2 Projects/Comprehensive Workflow for Large Histology Segmentation and Visualization

= Motivation =

3D histology stacks are being increasingly used to understand gross anatomical changes and to provide valuable educational contexts. Most existing toolkits allow a 2D approach and do not meet the challenges posed by 3D histology. ITKv4 can facilitate the realization application level toolkits that will allow for a sensible registration, segmentation and reconstruction of digital slides depicting various organs and tissue systems. We will leverage our extensive experience in constructing ITK-based tools to process 3D histology. Modules will be included that will allow for pre-processing (color correction, artifact removal, etc.), rigid and non-rigid registration, material-based segmentation, and visualization. Additionally, we will provide access to multi resolution data that describes ensembles of nephrons in a human kidney. Our team includes an anatomist who will provide validation data and will deploy the tool in her anatomy classes. Thus, our proposed tool will bring a valuable user community into the ITK fold.

= Goals =
 
= Data =

= Deliverables =
*New classes
**Color correction, artifact removal, image registration
= Team =

*Raghu Machiraju
*Kun Huang 
*Lisa Lee