trk_to_annotation

This repository provides utilities for converting .trk tractography files into Neuroglancer precomputed annotation format, and serving them locally with HTTP requests.

Install

python -m build
pip install .

Usage

python -m trk2annotation <trk_file> \
    --annotation_output_dir ./precomputed_annotations \
    --segmentation_output_dir ./precomputed_segmentations \
    --grid_densities 1 2 4 8 16

Arguments

Argument	Required	Default	Description
trk_file	✅	—	Path to the input .trk file
--annotation_output_dir	❌	./precomputed_annotations	Output directory for precomputed annotations
--segmentation_output_dir	❌	./precomputed_segmentations	Output directory for precomputed segmentations
--grid_densities	❌	[1, 2, 4, 8, 16]	Grid densities (powers of two, ascending order)

Running server for neuroglancer

Run the following command in the directory with your outputted folders

python -m trk_to_annotation.http_server

You should now be able to access the annotation and segmentation layers on neuroglancer via http://localhost:8000/