navis.average_skeletons¶

navis.average_skeletons(x, limit=10, base_neuron=None)[source]¶

Compute an average from a list of skeletons.

This is a very simple implementation which may give odd results if used on complex neurons. Works fine on e.g. backbones or tracts.

Parameters:

x (NeuronList) – Neurons to be averaged.
limit (int | str) – Max distance for nearest neighbour search. If the neurons have .units set, you can also pass a string such as e.g. “2 microns”.
base_neuron (neuron id | TreeNeuron, optional) – Neuron to use as template for averaging. If not provided, the first neuron in the list is used as template!

Return type:

TreeNeuron

Examples

>>> # Get a bunch of neurons
>>> import navis
>>> da2 = navis.example_neurons()
>>> # Prune down to longest neurite
>>> for n in da2:
...     if n.has_soma:
...         n.reroot(n.soma, inplace=True)
>>> da2_pr = da2.prune_by_longest_neurite(inplace=False)
>>> # Make average
>>> da2_avg = navis.average_skeletons(da2_pr, limit=10e3)
>>> # Plot
>>> da2.plot3d() 
>>> da2_avg.plot3d() 