navis.subset_neuron¶

navis.subset_neuron(x, subset, inplace=False, keep_disc_cn=False, prevent_fragments=False)[source]¶

Subset a neuron to a given set of nodes/vertices.

Note that for MeshNeurons it is not guaranteed that all vertices in subset survive because we will also drop degenerate vertices that do not participate in any faces.

Parameters:

x (TreeNeuron | MeshNeuron | Dotprops) – Neuron to subset.
subset (list-like | set | NetworkX.Graph | pandas.DataFrame) –
For TreeNeurons:
- node IDs to subset the neuron to
- a boolean mask
- DataFrame with node_id column
For MeshNeurons:
- vertex indices
- a boolean mask
For Dotprops:
- point indices
- a boolean mask
keep_disc_cn (bool, optional) – If False, will remove disconnected connectors that have “lost” their parent node/vertex.
prevent_fragments (bool, optional) – If True, will add nodes/vertices to subset required to keep neuron from fragmenting. Ignored for Dotprops.
inplace (bool, optional) – If False, a copy of the neuron is returned.

Return type:

TreeNeuron | MeshNeuron

Examples

Subset skeleton to all branches with less than 10 nodes

>>> import navis
>>> # Get neuron
>>> n = navis.example_neurons(1)
>>> # Get all linear segments
>>> segs = n.segments
>>> # Get short segments
>>> short_segs = [s for s in segs if len(s) <= 10]
>>> # Flatten segments into list of nodes
>>> nodes_to_keep = [n for s in short_segs for n in s]
>>> # Subset neuron
>>> n_short = navis.subset_neuron(n, nodes_to_keep)