Pipeline for 3D Reconstruction of Tau Burden Maps from MRI and Histology
- 3D Printing Cutting Molds
- Step 1. Convert 7T scan to NIFTI
- Step 2. Segment the MTL from background in ITK-SNAP
- Step 3. Create a reference mold
- Step 4. Find the correct rotation of the 7T image
- Step 5. Carve the tissue segmentation out of the mold
- Step 6. Generate Surface Mesh of the Mold
- Step 7. Simplify the STL file for 3D printing
- Step 8. Visualize mold and tissue in ParaView
- Data Organization
- WildCat Training and Whole-Slide Analysis
- Patch download and organization
- Train WildCat classifier in Jupyter
- Evaluate WildCat classifier on test patches
- Evaluate WildCat classifier on whole-slide image
- Validate WildCat classifier vs. Manual Ratings and Object Counts
- Training WildCat network from the command line
- Applying WildCat models in batch mode
- Whole-Slide Histology Processing