dvid.fetch.get_skeletons

dvid.fetch.get_skeletons(x, save_to=None, output='auto', on_error='warn', check_mutation=False, max_threads=5, progress=True, server=None, node=None)

Fetch skeleton for given body ID.

Parameters

• x (int | str | list thereof) – ID(s) of bodies for which to download skeletons. Also accepts pandas DataFrames if they have a body ID column.

• save_to (str | None, optional) – If provided, will save raw SWC to file. If str must be file or path.

• output ("auto" | "navis" | "swc" | None) –

  Determines the output of this function:

  • auto = navis.TreeNeuron if navis is installed else SWC table as pandas.DataFrame

  • navis = navis.TreeNeuron - raises error if navis not installed

  • swc = SWC table as pandas.DataFrame

  • None = no direct output - really only relevant if you want to only save the SWC to a file

• on_error ("warn" | "skip" | "raise") – What to do if fetching a skeleton throws an error. Typically this is because there is no skeleton for a given body ID but it could also be a more general connection error.

• check_mutation (bool, optional) – If True, will check if skeleton and body are still in-sync using the mutation IDs. Will warn if mismatch found.

• max_threads (int) – Max number of parallel queries to the dvid server.

• progress (bool) – Whether to show a progress bar or not.

• server (str, optional) – If not provided, will try reading from global.

• node (str, optional) – If not provided, will try reading from global.

Returns

• SWC (pandas.DataFrame) – Only if save_to=None else True.

• None – If no skeleton found.

See also

dvid.get_skeleton_mutation()

If you want to create a skeleton based on the current voxels yourself.

skeletonize_neuron()

Use this to create a skeleton from scratch - e.g. if there is no precomputed skeleton for a given body.

Examples

Fetch neuron as navis skeleton

>>> dt.get_skeleton(485775679)

Grab a neuron and save it directly to a file

>>> dt.get_skeleton(485775679, save_to='~/Downloads/', output=None)