navis.synapse_similarity¶

navis.synapse_similarity(x, sigma, omega, mu_score=True, restrict_cn=None, n_cores=1)[source]¶

Cluster neurons based on their synapse placement.

Distances score is calculated by calculating for each synapse of neuron A: (1) the (Euclidian) distance to the closest synapse in neuron B and (2) comparing the synapse density around synapse A and B. This is type-sensitive: presynapses will only be matched with presynapses, post with post, etc. The formula is described in Schlegel et al., eLife (2017):

$f(i_{s},j_{k}) = \exp(\frac{-d^{2}_{sk}}{2\sigma^{2}}) \exp(\frac{|n(i_{s})-n(j_{k})|}{n(i_{s})+n(j_{k})})$

The synapse similarity score for neurons i and j being the average of $f(i_{s},j_{k})$ over all synapses s of i. Synapse k is the closest synapse of the same sign (pre/post) in neuron j to synapse s. $d^{2}_{sk}$ is the Euclidian distance between these distances. Variable $\sigma$ (sigma) determines what distance between s and k is considered “close”. $n(i_{s})$ and $n(j_{k})$ are defined as the number of synapses of neuron i/j that are within given radius $\omega$ (omega) of synapse s and j, respectively (same sign only). This esnures that in cases of a strong disparity between $n(i_{s})$ and $n(j_{k})$ , the synapse similarity will be close to zero even if the distance between s and k is very small.

Parameters:

x (NeuronList) – Neurons to compare. Must have connectors.
sigma (int | float) – Distance between synapses that is considered to be “close”.
omega (int | float) – Radius over which to calculate synapse density.
mu_score (bool) – If True, score is calculated as mean between A->B and B->A comparison.
restrict_cn (int | list | None) – Restrict to given connector types. Must map to a type, relation or label column in the connector tables. If None, will use all connector types. Use either single integer or list. E.g. restrict_cn=[0, 1] to use only pre- and postsynapses.
n_cores (int) – Number of parallel processes to use. Defaults to half the available cores.

Return type:

pandas.DataFrame