A jupyter extension to visualize numpy arrays using Google's neuroglancer.
Make sure you meet the requirements of this extensions:
pip install -r requirements.txtThe extension itself is installed as a python module with the name nyroglancer:
python setup.py installFinally, 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.
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()Create ~/.pypirc with the following content:
[distutils]
index-servers=pypi
[pypi]
username=neuroglancer
password=xxxx
Run:
python setup.py sdist upload -r pypi