Tiny Jupyter Wrapper for neuroglancer viewer
Project description
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.
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