jupyter-neuroglancer

Simple Jupyter (and jupyter-server-proxy) integration with neuroglancer.

Pops up a neuroglancer viewer in a split pane in JupyterLab (via jupyterlab-sidecar) so you can more easily see real-time live visualizations driven by your python code.

When running on a remote JupyterHub, the viewer is automatically (and securely) proxied through jupyter-server-proxy so users get the exact same experience on theier local machine as well as a JupyterHub.

Installation

jupyter-neuroglancer is available on PyPI.

pip install jupyter-neuroglancer

Usage

jupyter_neuroglancer provides a display_in_sidecar function that accepts a regular neuroglancer Viewer object. You don't have to modify your neuroglancer code in any way!

import neuroglancer
from jupyter_neuroglancer import SidecarViewer

# Create a neuroglancer Viewer instance. This controls the visualization
viewer = neuroglancer.Viewer()

# Display the neuroglancer in JupyterLab as a sidecar
display_in_sidecar(viewer)

Using on a JupyterHub

When using this on a JupyterHub, you need jupyter-server-proxy installed in the image you are using. Since neuroglancer uses eventstreams for communication, you need it to be a version of jupyter-server-proxy that has this PR included. Until that PR is merged and released, you can install that with:

pip install --upgrade git+https://github.com/ganisback/jupyter-server-proxy@support-stream

Other than that, you do not have to modify your code in any way.