How to use Neuronvisio to select particular sections of a NEURON based multi-compartment model

Displaying and visualizing selected sections in multi-compartmental models in 3D it’s quite an hard task, however the info and the clarity that is possible to achieve is worth the effort.

Let’s say you have your multi-compartiment model ready in NEURON and you are interested to show in 3D selected sections of the model with arbitrary colors (for example, to show where certain stimuli are applied), like I did in my Medium Spiny Neuron model to show which spines get stimulated:

spiny MSN with stimulated with different trains in selected spines

Neuronvisio offers a nice API, from the visio module, accessible as controls.visio.select_sections(secs_list, scalar_value), which makes this operation easy.

For example, let’s take the pyramidal neuron model that comes as an example with Neuronvisio.

Let’s say that we want to select the soma, the iseg and the first section of the myelin, and we want to give them arbitrary colors.

To achieve that we can easily run:

controls.visio.select_sections([“soma”, “iseg”, “myelin[0]”], [1, 0.5, 0.2]), obtaining this picture:

Selecting and coloring special sections with Neuronvisio

Quite handy and pretty fast, don’t you think?