VFB-225 - Convert NRRD to Neuroglass friendly format #199
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request adds a complete client local pipeline for converting NRRD segmentation volumes to Neuroglancer precomputed format and generating 3D surface meshes. The main changes include two new Python scripts for conversion and mesh generation, and a comprehensive README with step-by-step instructions.
New conversion and mesh generation scripts:
convert_nrrd_to_precomputer.py: Converts NRRD files to Neuroglancer precomputed volumetric format, supporting multiple sources, automatic naming, voxel size detection, and optional compression.generate_meshes.py: Generates 3D meshes for all segments in precomputed volumes using marching cubes, sets up segment properties, updates metadata, and creates a Neuroglancer state JSON for easy visualization.