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NRRD to Neuroglancer Precomputed Workflow

Overview

This guide shows how to convert NRRD segmentation files to Neuroglancer precomputed format with meshes.

Fixed Issues

Issue #1: Meshes not showing in Neuroglancer

Root cause: Mesh vertices were in physical coordinates (microns) instead of voxel coordinates. Fix: Removed spacing parameter from marching_cubes() call. Neuroglancer applies resolution scaling separately.

Issue #2: Segmentation fragmentation

Clarification: The NRRD files contain multiple anatomical structures as separate segments (this is correct). If you see unexpected fragmentation, use merge_segments.py to consolidate connected components.

Workflow

Step 1: Inspect your data (optional but recommended)

cd /home/ddelpiano/git/neuroglass/dataScripts/nrrd_to_precomputed
python inspect_nrrd.py files/VFB_00101567.nrrd

Step 2: (Optional) Merge fragmented segments

Only use this if you want to merge disconnected pieces into single segments:

python merge_segments.py \
  files/VFB_00101567.nrrd \
  files/VFB_00101567_merged.nrrd \
  --min-size 100 \
  --verbose

Step 3: Convert NRRD to precomputed format

python converter.py \
  --input-dir files \
  --output-path output \
  --verbose

This will:

  • Find all .nrrd files in files/ directory
  • Convert each to precomputed format in output/ directory
  • Create a mapping file: output/sources_to_dataset.json

Step 4: Generate meshes

python meshes_generator.py \
  --input-path output \
  --dust-threshold 100 \
  --verbose

This will:

  • Find all precomputed datasets in output/ directory
  • Generate meshes for each segment (skipping segments < 100 voxels)
  • Create segment properties (labels and metadata)
  • Generate output/neuroglancer_state.json for easy loading

Step 5: Serve the data

cd output
npx http-server . -p 8080 --cors

Step 6: View in Neuroglancer

  1. Go to https://neuroglancer-demo.appspot.com/
  2. Click the {} (JSON) button in the top-right
  3. Copy the contents of output/neuroglancer_state.json
  4. Paste into the JSON editor
  5. Click outside the editor to load

Troubleshooting

Meshes still not showing?

  1. Check the browser console for errors
  2. Verify mesh files exist: 
    ls -lh output/*/mesh/
  3. Check segment IDs match: 
    python inspect_nrrd.py files/VFB_00101567.nrrd | grep "Segment IDs"
  4. Try loading a single segment manually in Neuroglancer UI

Segmentation looks wrong?

  • Use inspect_nrrd.py to see segment IDs and sizes
  • The NRRD files contain pre-labeled anatomical structures
  • If you see unexpected fragmentation, verify with the original data source

Performance issues?

  • Reduce --dust-threshold to skip more small segments
  • Generate meshes for fewer segments initially
  • Check your mesh file sizes