navis.split_axon_dendrite

navis.split_axon_dendrite(x, metric='synapse_flow_centrality', flow_thresh=0.9, split='prepost', cellbodyfiber=False, reroot_soma=True, label_only=False)

Split a neuron into axon and dendrite.

The result is highly dependent on the method and on your neuron’s morphology and works best for “typical” neurons.

Parameters:

• x (TreeNeuron | MeshNeuron | NeuronList) – Neuron(s) to split into axon, dendrite (and cell body fiber if possible).

• metric ('synapse_flow_centrality' | 'bending_flow' | 'segregation_index' | "flow_centrality", optional) –

  Defines which flow metric we will try to maximize when splitting the neuron(s). There are four flavors:

  • ’synapse_flow_centrality’ via synapse_flow_centrality() (note that this metric was previously called just “flow_centrality”)

  • ’bending_flow’ via bending_flow()

  • ’segregation_index’ via arbor_segregation_index()

  • ’flow_centrality’ via flow_centrality()

  Will try using existing columns in the node table. If not present, will invoke the respective functions with default parameters. All but flow_centrality require the neuron to have connectors.

• flow_thresh (float [0-1]) – The “linker” between axon and dendrites will be the part of the neuron with the highest flow (see metric). We define it by max(flow) * flow_thresh. You might have to decrease this value for atypical or not well segregated neurons.

• split ('prepost' | 'distance') –

  Method for determining which compartment is axon and which is the dendrites:

  • ’prepost’ uses number of in- vs. outputs

  • ’distance’ assumes the compartment proximal to the soma is the dendrites

• cellbodyfiber ("soma" | "root" | False) –

  Determines whether we will try to find a cell body fiber (CBF).

  • ”soma” will try finding the CBF only if the neuron has a soma

  • ”root” will consider the root to be the source of the CBF as fallback if there is no soma

  • False will not attempt to extract the CBF

  A CBF is something typically found in insect neurons which are not bipolar unlike most vertebrate neurons but rather have a passive soma some distance away from axon/dendrites.

• reroot_soma (bool,) – If True and neuron has a soma, will make sure the neuron is rooted to its soma.

• label_only (bool,) – If True, will not split the neuron but rather add a “compartment” column to the node and connector table of the input neuron.

• parallel (bool) – If True and input is NeuronList, use parallel processing. Requires pathos.

• n_cores (int, optional) – Numbers of cores to use if parallel=True. Defaults to half the available cores.

• progress (bool) – Whether to show a progress bar. Overruled by navis.set_pbars.

• omit_failures (bool) – If True will omit failures instead of raising an exception. Ignored if input is single neuron.

Returns:

Axon, dendrite, linker and CBF (the latter two aren’t guaranteed). Fragments will have a new property compartment (see example).

Return type:

NeuronList

Examples

>>> import navis
>>> x = navis.example_neurons(1)
>>> split = navis.split_axon_dendrite(x, metric='synapse_flow_centrality',
...                                   reroot_soma=True)
>>> split                                                   
<class 'navis.NeuronList'> of 3 neurons
                      neuron_name  id  n_nodes  n_connectors  compartment
0                  neuron 123457   16      148             0         axon
1                  neuron 123457   16     9682          1766       linker
2                  neuron 123457   16     2892           113     dendrite
>>> # For convenience, split_axon_dendrite assigns colors to the resulting
>>> # fragments: axon = red, dendrites = blue, CBF = green
>>> _ = split.plot3d(color=split.color)

Alternatively just label the compartments

>>> x = navis.split_axon_dendrite(x, label_only=True)
>>> x.nodes[~x.nodes.compartment.isnull()].head()           
         node_id label        x        y        z     radius  parent_id  type compartment
110      111     0  17024.0  33790.0  26602.0  72.462097        110  slab      linker
111      112     0  17104.0  33670.0  26682.0  72.462097        111  slab      linker
112      113     0  17184.0  33450.0  26782.0  70.000000        112  slab      linker
113      114     0  17244.0  33270.0  26822.0  70.000000        113  slab      linker
114      115     0  17324.0  33150.0  26882.0  74.852798        114  slab      linker

See also

navis.heal_skeleton()

Axon/dendrite split works only on neurons consisting of a single tree. Use this function to heal fragmented neurons before trying the axon/dendrite split.