Octarine NAVis Plugin

This plugin enables Octarine to visualize NAVis data such as skeletons, meshes, volumes, etc.

Installation

pip install octarine-navis-plugin -U

Note that you will have to install Octarine and NAVis separately! This is intentional so that you can choose the install options (e.g. the Window manager) yourself.

Usage

The plugin will automatically be loaded alongside Octarine and extends the functionality by:

1. Allowing to pass navis.Neuron/Lists, navis.Volumes and skeletor.Skeletons to the generic Viewer.add() method.
2. Adding a dedicated Viewer.add_neurons method with various specialized parameters that shadow the options in navis.plot3d.

import navis
import octarine as oc

# Initialize the viewer
v = oc.Viewer()

# Grab some neurons
n = navis.example_neurons(5, kind='mesh')

# Add them to the viewer
v.add(n)

# Alternatively use the specialized method with additional options
navis.strahler_index(n)
v.clear()
v.add_neurons(n, color_by='strahler_index', palette='viridis')