fafbseg.flywire.skid_to_id#

fafbseg.flywire.skid_to_id(x, sample=None, catmaid_instance=None, progress=True, *, dataset=None)[source]#

Find the FlyWire root ID for a given (FAFB) CATMAID neuron.

This function works by:

  1. Fetch the skeleton for given CATMAID neuron.

  2. Transform the skeleton to FlyWire space.

  3. Map the x/y/z location of the skeleton nodes to root IDs.

  4. Return the root ID that was seen the most often.

Parameters:

  • x (int | list-like | str | TreeNeuron/List) – Anything that’s not a TreeNeuron/List will be passed directly to pymaid.get_neuron.

  • sample (int | float, optional) – Number (>= 1) or fraction (< 1) of skeleton nodes to sample to find FlyWire root IDs. If None (default), will use all nodes.

  • catmaid_instance (pymaid.CatmaidInstance, optional) – Connection to a CATMAID server. If None, will use the current global connection. See pymaid docs for details.

  • progress (bool) – If True, shows progress bar.

  • dataset ("public" | "production" | "sandbox" | "flat_630", optional) – Against which FlyWire dataset to query. If None will fall back to the default dataset (see set_default_dataset()).

Returns:

Mapping of skeleton IDs to FlyWire root IDs. Confidence is the difference between the frequency of the root ID that was seen most often and the second most seen ID.

Return type:

pandas.DataFrame

See also

neuron_to_segments()

Takes already downloaded and transformed neuron(s) and returns corresponding FlyWire root IDs.

Examples

>>> from fafbseg import flywire
>>> import pymaid
>>> # Connect to the VFB's CATMAID
>>> rm = pymaid.CatmaidInstance('https://fafb.catmaid.virtualflybrain.org/',
...                             project_id=1, api_token=None)
>>> roots = flywire.skid_to_id([6762, 2379517])
>>> roots
  skeleton_id          flywire_id  confidence
0        6762  720575940608544011        0.80
1     2379517  720575940617229632        0.42