navis.interfaces.neuprint.fetch_mesh_neuron¶
- navis.interfaces.neuprint.fetch_mesh_neuron(x, *, lod=1, with_synapses=False, missing_mesh='raise', parallel=True, max_threads=5, seg_source=None, client=None, **kwargs)[source]¶
Fetch mesh neuron.
Requires additional packages depending on the mesh source.
For DVID you need dvid-tools:
pip3 install dvidtools
For everything else you need cloudvolume:
pip3 install cloud-volume
- 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.
lod (int) – Level of detail. Higher
lod
= coarser. Ignored if mesh source is DVID.with_synapses (bool, optional) – If True will download and attach synapses as
.connectors
.missing_mesh ('raise' | 'warn' | 'skip') –
What to do if no mesh 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.
seg_source (str | cloudvolume.CloudVolume, optional) – Use this to override the segmentation source specified by neuPrint.
client (neuprint.Client, optional) – If
None
will try using global client.**kwargs – Will be passed to
cloudvolume.CloudVolume
.
- Returns:
Containing
navis.MeshNeuron
. Note that meshes are resized to raw voxel size to match other spatial data from neuprint (synapses, skeletons, etc).- Return type:
navis.Neuronlist