Skelescope

A simple interactive 3D skeleton viewer for Jupyter

Development installation

Create a virtual environment and install skelescope's development dependencies:

poetry install
poetry shell

You then need to install the JavaScript dependencies and run the development server.

npm install
npm run dev

All is set to open example.ipynb in JupyterLab, VS Code, or your favorite editor to start developing. Any change made in the js folder will be directly reflected in the notebook.

Deploy to PyPi

poetry build -vvv
poetry publish

Proposed Interface (Jakob, edited pha)

viewer = NeuriteViewer(
  width = "500", # non-required value. defaults to filling the widget
  height = "300"
)

# add neuron to viewer instance
viewer.loadNeuron(
  swc, # swc in JSON format
  synapses, # JSON format (position, [pre_post_annotation, graph_node_id])
  tree_topology = None
  cache_folder = None 
  name = None, # not required, defaults to "<root_id>"
  neuronColor, # not required, defaults to random color
  synapseColor, # not required
  recenter_camera=True # not required
)

# synapses are attached to the neuron as neuron.connectors.

# remove neuron from instance
viewer.deleteNeuron(
  name # can be manually assigned name or <root_id>
)

viewer.getNeuronSelection(
  names # list of all neuron names to get selection from, not required parameter
)

viewer.getSegmentSelection(
  names # list of all neuron names to get selection from, not required parameter
)

viewer.getSynapseSelection(
  names # # list of all neuron names to get synapse selection from, not required parameter
)

viewer.show() # renders the widget