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Neuroglancer Jupyter Extension

A jupyter extension to visualize numpy arrays using Google's neuroglancer.

Installation

Make sure you meet the requirements of this extensions:

pip install -r requirements.txt

The extension itself is installed as a python module with the name nyroglancer:

python setup.py install

Finally, the extension has to be enabled in jupyter. Add to ~/.jupyter/jupyter_notebook_config.py the module nyroglancer.extension, e.g.:

c = get_config()
c.NotebookApp.server_extensions = ['nyroglancer.extension']

or if ~/.jupyter/jupyter_notebook_cofig.json exists, you can add nyroglancer.extension to the server_extensions field.

These config options work as of 5/9/17 with the following package versions:

  • Jupyer: 4.3.0
  • IPython: 5.1.0
  • nbformat: 4.3.0

Try updating nbformat if you have problems - if that fails you may want to check out the docs on the Jupyter config system, as it seems to change frequently.

Usage

In your notebook, create a nyroglancer.Viewer and populate it with the numpy arrays you'd like to visualize. The following snippet shows how to read numpy arrays from an HDF5 file and show them:

import nyroglancer
import h5py

raw = h5py.File("test.hdf")['volumes/raw']
seg = h5py.File("test.hdf")['volumes/labels/neuron_ids']

viewer = nyroglancer.Viewer()
viewer.add(raw, resolution=[40,4,4], name="raw")
viewer.add(seg, resolution=[40,4,4], name="neuron IDs")
viewer.show()

Publishing to PyPI

Create ~/.pypirc with the following content:

[distutils]
index-servers=pypi

[pypi]
username=neuroglancer
password=xxxx

Run:

python setup.py sdist upload -r pypi