navis.interfaces.microns.get_somas¶

navis.interfaces.microns.get_somas(root_ids, table='nucleus_neuron_svm', datastack='cortex65')[source]¶

Fetch somas based on nuclei segmentation for given neuron(s).

Since this is a nucleus detection you will find that some neurons do not have an entry despite clearly having a soma. This is due to the “avocado problem” where the nucleus is separate from the rest of the soma.

Important

This data currently only exists for the ‘cortex65’ datastack (i.e. “minnie65_public_v117”).

Parameters:

root_ids (int | list of ints | None) – Root ID(s) for which to fetch soma infos. Use None to fetch complete list of annotated nuclei.
table (str) – Which table to use for nucleus annotations.
datastack ("cortex65" | "cortex35" | "layer 2/3") – Which dataset to use. Internally these are mapped to the corresponding sources (e.g. “minnie65_public_v117” for “cortex65”).

Returns:

Pandas DataFrame with nuclei (see Examples). Root IDs without a nucleus will simply not have an entry in the table.

Return type:

DataFrame