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
  • Set up directory structure
  • Preparing the 7T MRI
  • Preparing the 9.4T MRI
  • Preparing the blockface images
  • Preparing the histology data
• Data Organization (PATCH|Lab PMACS cluster)
  • Understanding the directory structure
  • Checking Input Files for Specimen
  • Preparing the 7T MRI
  • Preparing the 9.4T MRI
  • Preparing the blockface images
  • Preparing Histology
• 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
  • Converting to OpenSlide compatible format
• Managing Histology Tasks with `svs_to_cloud.sh`
  • Checking for New Scanned Slides (check_for_new_slides_all)
  • Updating Histology Manifest Files (update_histo_match_manifest_all)
  • Preprocessing Histology Slides (preprocess_slides_all)
  • Running WildCat in GCP (density_map_all)
  • Extracting NISSL DeepCluster feature maps (nissl_multichannel_all)
  • Importing histology-derived maps (rsync_histo_all)
  • Troubleshooting:
• Running 3D Reconstruction
  • Check the inputs
  • Generate masks for histology
  • MRI processing (7T to 9.4T registration)
  • Run blockface reconstruction
  • Training a custom random forest classifier
  • Compute initial blockface to MRI matching
  • Run blockface to MRI registration
  • Histology Mask Generation
  • MRI-Guided Nissl 3D Reconstruction
  • IHC to Nissl Registration
  • Generating 3D WildCat density reconstructions
• Tips and Tricks
  • Working with remote ITK-SNAP workspaces

Indices and tables

• Index

• Module Index

• Search Page