neuroglancer-volume-viewer 0.1.0

Launch a Neuroglancer viewer for 3D data stored in a Zarr file.

This repository contains scripts that launch a Neuroglancer viewer to visualize 3D data stored in a Zarr file, making it accessible via a web browser.

Using Neuroglancer with Zarr files is particularly useful for viewing very large datasets, because the lazy loading scheme prevents the entire array from being loaded into memory.

• open-zarr-file-remote — run the viewer on a remote machine and view it locally via an SSH tunnel.
• open-zarr-file_local — run the viewer on the same machine you'll view it on (no SSH tunnel needed).

Remote use: open-zarr-file-remote

In this example, I am using port 9090:

1. Create the SSH tunnel

ssh -L 9090:localhost:9090 -Y my-remote-machine

2. Run the script (the port must match the SSH tunnel port)

open-zarr-file-remote 9090 /path/to/file.zarr

3. This script will print the URL where you can access the neuroglancer viewer on your local machine. It will look something like this: Open in browser: http://localhost:9090/v/14a31d6d2d4d11d95fa35f51daadc97da9100571/. Open the link in your browser on your local machine.

Local use: open-zarr-file-local

When the zarr file lives on the same machine you'll view it on, no SSH tunnel or port is needed — neuroglancer picks a free port itself:

open-zarr-file-local /path/to/file.zarr

The script will print a URL like Open in browser: http://127.0.0.1:46789/v/14a31d6d2d4d11d95fa35f51daadc97da9100571/. Open it in your browser.

Optional resolution argument

Both scripts accept an optional voxel resolution (in nanometers) as the last argument. For example:

open-zarr-file-remote 9090 /path/to/file.zarr 10
open-zarr-file-local /path/to/file.zarr 10

Input file types

This package expects data in the zarr format. Zarr version 3 and zarr version 2 are supported. If using zarr version 2, the data must be saved with name 'data'.

Example of how to save zarr v2 files:

import zarr
root = zarr.open_group("/path/to/file.zarr", mode='w', zarr_format=2)
root.create_array('data', data=array)

neuroglancer-volume-viewer works with zarr files saved using methods from the pyxalign package.