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Neuroglancer Python Integration

This package provides a Python interface for controlling Neuroglancer, a web-based 3-d volumetric data viewer.

The following features are supported:

  • Viewing in-memory NumPy arrays (or any other array type with a similar interface, including HDF5 arrays loaded through h5py)
  • Reading and writing the Neuroglancer viewer state from Python
  • Changing Neuroglancer key and mouse bindings
  • Defining actions (to be triggered by key or mouse bindings) that cause a Python callback to be invoked.

It starts a local web server for communicating state changes using sockjs, serving a copy of the Neuroglancer client code, and for serving data to the Neuroglancer client if Python data sources are used.

Example

See the example programs in the examples/ directory. Run them using the Python interpreter in interactive mode, e.g.

python -i example.py

or using the IPython magic command

%run -i python.py

Do not run an example non-interactively as

python example.py

because then the server will exit immediately.

Mesh generation

For in-memory segmentation volumes, mesh representations of the surface of each object can be generated on-demand as they are requested by the client (e.g. due to the user selecting a segment). This requires that the C++ extension module be built. If you install this Python package normally, that will happen automatically. For development, see the instructions below.

Security

By default the server binds only to the 127.0.0.1 address, and for protection against cross-site scripting attacks only accepts requests that include a valid randomly-generated 160-bit secret key.

Development

First, make sure NumPy is installed. If using a virtual environment (which is recommended), run:

pip install numpy

Building the C++ extension module

Mesh generation for segmentation volumes depends on a C++ extension module. To build it, activate a suitable Python virtual environment and run:

python setup.py develop

Serving the Neuroglancer client code

By default, a bundled copy of the Neuroglancer client code (HTML, CSS, JavaScript) is served from the neuroglancer/static directory. You can build this bundled copy by running

python setup.py bundle_client

This requires a suitable version of Node.js, as dsecribed in the top level README. The PyPI package includes a prebuilt copy of these files.

The Neuroglancer client code can also be served from several other locations, for convenience during development.

For example, while developing the Neuroglancer client, you can run the shell command

npm run dev-server-python

to start the webpack-dev-server on http://localhost:8080 and then call

neuroglancer.set_static_content_source(url='http://localhost:8080')

from Python. With this setup, refreshing the browser will automatically reflect any changes to the client source code.

Publishing to PyPI

This package is maintained at PyPI.

To upload a new version, create a ~/.pypirc file with the following content:

[distutils]
index-servers =
  pypi
  testpypi

[pypi]
username=neuroglancer
password=xxxx

[pypitest]
repository=https://test.pypi.org/legacy/
username=neuroglancer
password=xxxx

To publish a new version, run the following command:

python setup.py bundle_client sdist
twine upload dist/*