navis.break_fragments¶

navis.break_fragments(x, labels_only=False, min_size=None)[source]¶

Break neuron into its connected components.

Neurons can consists of several disconnected fragments. This function turns these fragments into separate neurons.

Parameters:

x (TreeNeuron | MeshNeuron) – Fragmented neuron.
labels_only (bool) – If True, will only label each node/vertex by which fragment it belongs to. For TreeNeurons, this adds a “fragment” column and for MeshNeurons, it adds a .fragments property.
min_size (int, optional) – Fragments smaller than this (# of nodes/vertices) will be dropped. Ignored if labels_only=True.

Return type:

NeuronList

See also

navis.heal_skeleton(): Use to heal fragmentation instead of breaking it up.

Examples

>>> import navis
>>> n = navis.example_neurons(1)
>>> # Artifically disconnect parts of the neuron
>>> n.nodes.loc[100, 'parent_id'] = -1
>>> # Break into fragments
>>> frags = navis.break_fragments(n)
>>> len(frags)
2