Replacement of real axon with simplified segments. Reasons?


I am actually using some of the neuronal models in the database for simulations using NEURON, and have not clearly understood why the real reconstructed, complex axon is replaced with a simplified one in almost your models of pyramidal neurons.

Many thanks for the answer,
Dr. Cassara’



The replacement of the axons by a shorter version that only represents the axon initial segment / hillock is a simplification for mostly computational reasons. Simulating the full axons would add a lot of compartments to simulation which increase the memory and compute requirements. Our current assumption is that not much computation is happening in the axon, and that the APs are submitted without much modification. Of course this is, as mentioned, a simplification and can be refined in the future. E.g. in the next release of the circuit we will include already some myelinated cable after the AIS to avoid boundary effects.

In practice, during the simulation when an AP is generated, this information is sent immediately to the relevant synapses of the postsynaptic cell with a delay that is calculated based on the path length along the full axon toward the synapse.

Werner Van Geit
Blue Brain Project


Dear Werner Van Geit,
Thank you for the answer. I am aware that for many studies the modeling of only the AIS is sufficient, but for many other purposes the modeling of the whole axonal three with its branches is relevant. This is the case for example in my studies related to the response of single neurons to external electric fields. The EM-Neuro coupling happens all over the body, and the large extension of the axonal three may have a relevant contribution to neurostimulation. I would be extremely interested in more extended neuronal models with reconstructed and parametrized axonal threes.

Best Regards,