Managing a model cell with complex anatomy

The CellBuilder can be very helpful for specifying the spatial grid and biophysical properties of cell models that are based on detailed morphometric reconstructions. In this tutorial, we will construct a model cell that borrows the anatomy of the pyramidal neuron that is included with NEURON's demonstration program.

We'll use the CellBuilder to assign these biophysical properties to our model:

Section

Biophysics

Notes

soma

hh

---

axon

hh

---

basilar dendrites

pas

e_pas = -65 mV
g_pas = 3.333e-5 S / cm² (Rm = 30,000 ohm cm²)

apical dendrites

pas

same as basliar dendrites

reduced hh

gnabar_hh and gkbar_hh reduced to 10%
gl_hh = 0 (already has g_pas)

Throughout the cell cm = 1 uf/cm², Ra = 160 ohm cm.

We will follow this sequence of steps.

Step 1. Get the cell's anatomy into a CellBuilder

Step 2. Create subsets

Step 3. Specify the spatial grid

Step 4. Specify biophysics
Set up a strategy for specifying biophysics
Execute the strategy

Step 5. Use the model specification

Go back to the main page ("Using the Cell Builder") to work on a different tutorial.

Section	Biophysics	Notes
soma	hh	---
axon	hh	---
basilar dendrites	pas	e_pas = -65 mV g_pas = 3.333e-5 S / cm² (Rm = 30,000 ohm cm²)
apical dendrites	pas	same as basliar dendrites
	reduced hh	gnabar_hh and gkbar_hh reduced to 10% gl_hh = 0 (already has g_pas)