ngretrieve ⤵️

Script to retrieve a crop based on annotations in a Neuroglancer state (either the URL or the JSON file). Works with either a point cloud, or one or several lines/bounding boxes.

Dependencies

• cloud-volume[zarr]
• neuroglancer
• numpy

Install all of them with:

pip install 'cloud-volume[zarr]' neuroglancer numpy

Usage

Pass either a Neuroglancer URL (--url) between single quotes or the path to a JSON file with a Neuroglancer state (--json).

python download_from_annotation.py --url 'https://neuroglancer-demo.appspot.com/#!...' --volume_layer_name "layer1" --annotation_layer_name "layer2" [--output_dir '/path/to/output/'] [--margin 50] [--log]

python download_from_annotation.py --json '/path/to/state.json' --volume_layer_name "layer1" --annotation_layer_name "layer2" [--output_dir '/path/to/output/'] [--margin 50] [--log]