fafbseg.flywire.get_skeletons#

fafbseg.flywire.get_skeletons(root_id, threads=2, omit_failures=None, max_threads=6, dataset=783, progress=True)[source]#

Fetch precomputed skeletons.

Currently this only works for proofread (!) 630 and 783 root IDs (i.e. the first two public releases of FlyWire).

Parameters:

  • root_id (int | list of ints | NeuronCriteria) – Root ID(s) of the FlyWire neuron(s) you want to skeletonize. Must be root IDs that existed at materialization 630 or 783 (see dataset parameter).

  • omit_failures (bool, optional) –

    Determine behaviour when skeleton generation fails (e.g. if the neuron has only a single chunk):

    • None (default) will raise an exception

    • True will skip the offending neuron (might result in an empty NeuronList)

    • False will return an empty TreeNeuron

  • dataset (630 | 783) – Which dataset to query.

  • progress (bool) – Whether to show a progress bar.

  • max_threads (int) – Number of parallel requests to make when fetching the skeletons.

Returns:

skeletons – Either a single neuron or a list thereof.

Return type:

navis.NeuronList | navis.TreeNeurons

See also

skeletonize_neuron()

Use this function to skeletonize neurons from scratch, e.g. if there aren’t any precomputed skeletons available.

Examples

>>> from fafbseg import flywire
>>> n = flywire.get_skeletons(720575940603231916)
>>> n                                                   
type                                             navis.TreeNeuron
name                                                     skeleton
id                                             720575940603231916
n_nodes                                                      3588
n_connectors                                                 None
n_branches                                                    586
n_leafs                                                       645
cable_length                                           2050971.75
soma                                                         None
units                                                 1 nanometer
dtype: object