Table Of Contents
Table Of Contents

fafbseg.flywire.skeletonize_neuron

fafbseg.flywire.skeletonize_neuron(x, drop_soma_hairball=True, contraction_kws={}, skeletonization_kws={}, radius_kws={}, assert_id_match=False, dataset='production')[source]

Skeletonize flywire neuron.

Parameters

  • x (int | trimesh.TriMesh) – ID or trimesh of the flywire neuron you want to skeletonize.

  • drop_soma_hairball (bool) – If True, we will try to drop the hairball that is typically created inside the soma.

  • contraction_kws (dict) – Optional parameters for the contraction phase. See skeletor.contract.

  • skeletonization_kws (dict) – Optional parameters for the skeletonization phase. See skeletor.skeletonize.

  • radius_kws (dict) – Optional parameters for the radius extraction phase. See skeletor.radius.

  • assert_id_match (bool) – If True, will check if skeleton nodes map to the correct segment ID and if not will move them back into the segment. This is potentially very slow!

  • dataset (str | CloudVolume) –

    Against which flywire dataset to query::

    • ”production” (current production dataset, fly_v31)

    • ”sandbox” (i.e. fly_v26)

Returns

The extraced skeleton, simplified and contracted mesh, respectively.

Return type

skeleton, simpified_mesh, contracted_mesh

Examples

>>> tn, simp, cntr = flywire.skeletonize_flywire_neuron(720575940614131061)
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