pymaid.get_partners_in_volume

pymaid.get_partners_in_volume(x, volume, syn_threshold=None, min_size=2, remote_instance=None)[source]

Retrieve the synaptic/gap junction partners within a CATMAID Volume.

Important

Connectivity (total number of connections) returned is restricted to that volume.

Parameters:

  • x –

    Neurons to check. Can be either:

    1. list of skeleton ID(s) (int or str)

    2. list of neuron name(s) (str, exact match)

    3. an annotation: e.g. ‘annotation:PN right’

    4. CatmaidNeuron or CatmaidNeuronList object

  • volume (str | list of str | navis.Volume) – Name of the CATMAID volume to test OR volume dict with {‘vertices’:[],’faces’:[]} as returned by e.g. get_volume().

  • syn_threshold (int, optional) – Synapse threshold. This threshold is applied to the TOTAL number of synapses across all neurons!

  • min_size (int, optional) – Minimum node count of partner (default = 2 -> hide single-node partner).

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

Returns:

DataFrame in which each row represents a neuron and the number of synapses with the query neurons:

 neuron_name  skeleton_id  num_nodes    relation     skid1  skid2 ...
1  name1         skid1    node_count1   upstream     n_syn  n_syn ..
2  name2         skid2    node_count2  downstream    n_syn  n_syn .
3  name3         skid3    node_count3  gapjunction   n_syn  n_syn .

  • Relation can be: upstream (incoming), downstream (outgoing) of the neurons of interest or gap junction

  • partners can show up multiple times if they are e.g. pre- AND postsynaptic

  • the number of connections between two partners is restricted to the volume

Return type:

pandas.DataFrame

See also

get_neurons_in_volume()

Get all neurons within given volume.

filter_connectivity()

Filter connectivity table or adjacency matrix by volume(s) or to parts of neuron(s).