Octarine plugin to visualize NAVis data in 3D.
Project description
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 to keep the dependencies light.
Usage
The plugin will automatically be loaded alongside Octarine
and extends the functionality by:
- Allowing to pass
navis.Neuron/Lists
,navis.Volumes
andskeletor.Skeletons
to the genericViewer.add()
method. - Adding a dedicated
Viewer.add_neurons
method with various specialized parameters that shadow the options innavis.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')
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