pymaid.get_annotated

pymaid.get_annotated(x, include_sub_annotations=False, raise_not_found=True, allow_partial=False, remote_instance=None)[source]

Retrieve entities (neurons + annotations) with given annotation(s).

This works similar to CATMAID’s neuron search widget: multiple annotations are intersected! Includes meta-annotations.

Parameters:

  • x (str | list of str) – (Meta-)annotations(s) to search for. Like CATMAID’s search widget, you can use regex to search for names by starting the query with a leading /. Use a leading ~ (tilde) to indicate NOT condition.

  • include_sub_annotations (bool, optional) – If True, will include entities that have annotations meta-annotated with x. Does not work on NOT search conditions.

  • allow_partial (bool, optional) – If True, partially matching annotations are searched too.

  • raise_not_found (bool, optional) – If True raise Exception if no match for any of the query annotations is found. Else log warning.

  • remote_instance (CatmaidInstance, optional) – If not passed directly, will try using global.

Returns:

DataFrame in which each row represents an entity:

  id  name  skeleton_ids type
0
1
2
...

Return type:

pandas.DataFrame

See also

pymaid.find_neurons()

Use to retrieve neurons by combining various search criteria. For example names, reviewers, annotations, etc.