Question: Adding specific annotation (metadata tags) to mass imports of swcs to Catmaid

[Mohinta2892]

Hi!

To upload selected skels into a CATMAID instance, I am currently running the below:

resp = pymaid.upload_neuron(n, source_type=None, remote_instance=rm)

Once imported, it saves Import as the annotated as metadata tag.
I wish to modify this tag per the class name of my selected skels, for example, segmented-KCs.

Do I need to modify the TreeNeuron object to have this as a value to any attribute?

Best,
Samia

[clbarnes]

Yes, to annotate an uploaded CatmaidNeuron you can modify its annotations list, and then set import_annotations=True in upload_neuron.

[Mohinta2892]

Thanks Chris.

n = TreeNeuron

In it's attributes this is all I see:

{'nodes': <class 'pandas.core.frame.DataFrame'>, 'graph': 'nx.DiGraph', 'igraph': 'igraph.Graph', 'n_branches': <class 'int'>, 'n_leafs': <class 'int'>, 'cable_length': typing.Union[int, float], 'segments': typing.List[list], 'small_segments': typing.List[list], 'root': <class 'numpy.ndarray'>, 'soma': typing.Union[int, str, NoneType], 'soma_pos': typing.Union[typing.Sequence, NoneType], 'soma_detection_radius': typing.Union[float, int, pint.util.Quantity], 'soma_detection_label': typing.Union[float, int, str], 'soma_radius': typing.Union[float, int, str], '_soma': typing.Union[typing.Callable[[ForwardRef('TreeNeuron')], typing.Sequence[int]], int], 'tags': typing.Union[typing.Dict[str, typing.List[int]], NoneType]}

Do I then need to wrap it back to be a Catmaid neuron and then edit the annotations list?
Also, because we are uploading, this neuron does not contain any annotations. Need to assign it so that it uploads with that annotation, rather than a generic Import.

[clbarnes]

Yes, looks like TreeNeurons don't have any annotations, but IIRC you can just do CatmaidNeuron(my_tree_neuron) and it should all work, then update the annotations on the new object.