navis.interfaces.neuprint.fetch_skeletons¶

navis.interfaces.neuprint.fetch_skeletons(x, *, with_synapses=False, heal=False, missing_swc='raise', parallel=True, max_threads=5, client=None)[source]¶

Construct navis.TreeNeuron/List from neuprint neurons.

Notes

Synapses will be attached to the closest node in the skeleton.

Parameters:

x (str | int | list-like | pandas.DataFrame | SegmentCriteria) – Body ID(s). Multiple Ids can be provided as list-like or DataFrame with “bodyId” or “bodyid” column.
with_synapses (bool, optional) – If True will also attach synapses as .connectors.
heal (bool | int | float, optional) – If True, will automatically heal fragmented skeletons using neuprint-python’s heal_skeleton function. Pass a float or an int to limit the max distance at which nodes are allowed to be re-connected (requires neuprint-python >= 0.4.11).

missing_swc ('raise' | 'warn' | 'skip') –

What to do if no skeleton is found for a given body ID:

"raise" (default) will raise an exception
"warn" will throw a warning but continue
"skip" will skip without any message

parallel (bool) – If True, will use parallel threads to fetch data.
max_threads (int) – Max number of parallel threads to use.
client (neuprint.Client, optional) – If None will try using global client.

Return type:

navis.Neuronlist