Creating a stylized ("stick-figure") model cell

Our goal is to build an extremely simplified model of a pyramidal cell.

This model will have a soma, an apical dendritic tree with a primary trunk and two distal branches, a basilar tree that is lumped into a single equivalent cylinder, and an axon (see table for dimensions). The soma and axon will have HH spike currents at normal density. The apical dendrites will also have spike currents, but only at 10% of the density in the soma and axon. The basilar dendrites are to be passive.

Geometry

Section L
(um) diam
(um) Biophysics

soma 20 20 hh

ap[0] 400 2 reduced hh*

ap[1] 300 1 reduced hh*

ap[2] 500 1 reduced hh*

bas 200 3 pas

axon 800 1 hh

*--In the apical dendrites, gnabar_hh and gkbar_hh are reduced to 10% of normal,
and el_hh (equilibrium potential of the hh leak current) is changed to -64 mV.
In the basilar dendrite, e_pas is -65 mV. With these values, resting potential is
approximately -65 mV throughout the cell.
Other parameters: cm = 1 uf/cm², Ra = 160 ohm cm.

We will follow this sequence of steps.

Step 1. Bring up a CellBuilder

Step 2. Specify topology

Step 3. Specify subsets

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

Step 5. Specify biophysics
Set up a strategy for specifying biophysics
Execute the strategy

Step 6. Use the model specification

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

	Geometry
Section	L (um)	diam (um)	Biophysics
soma	20	20	hh
ap[0]	400	2	reduced hh*
ap[1]	300	1	reduced hh*
ap[2]	500	1	reduced hh*
bas	200	3	pas
axon	800	1	hh