ng-slice-download

A simple command line utility to download the current neuroglancer view to a local TIFF file, with minimal compute requirements.

Usage

1. Install uv
2. Open an OME-Zarr or N5 image in neuroglancer, and navigate to the 2D view that you want to download. Important: the view to be downloaded is in the upper left panel.
3. Copy the full neuroglancer link from the browser
4. Run:

uvx ng-slice-download '[full neuroglancer link]'

replacing [full neuroglancer link] with your neuroglancer link. It's important to surround the neuroglancer link in quotes because it will probably contain special characters.

Command documentation

% ng-slice-download --help
Usage: ng-slice-download [OPTIONS] NEUROGLANCER_URL

Options:
  --output-dir PATH    Directory to download image files to.
  --skip-lowres-check  Skip the low resolution check.
  --help               Show this message and exit.

Changelog

0.2

• Ask before overwriting output TIFF files (.zarr files are still overwritten without asking)
• Saved images use the Neuroglancer layer name in the filename
• Added support for N5 images.
• Renamed the --output_dir flag to --output-dir.
• Add --skip-lowres-check option to skip the initial low resolution check that the orientation is correct.
• Add a more helpful error message if selected layer is not an image layer.
• Allow layers with a transform, but without a transformation matrix.

0.1.1

First release