Qroid_montreal wrote:I Imported the Mainen and Sejnowski 1996 L5 pyramidal cell model into Cell Builder
Actually, you have to be careful about that. The code in demofig1.hoc takes into account the contribution of spines to surface area by distorting cell morphology (the "folding factor" approach described by Jack et al (1989) and Major et al. (1994)). It's a perfectly legitimate way to make the equations work out, but if you then import that distored morphology into a CellBuilder, the result is a model cell in which none of the diamters or lengths is the same as the biological original.
the morphometric data looks right in the shape plot.
Appearances can be deceptive. Consider the L5 pyramidal cell. Using the original morophometric data, the long primary apical branch that bifurcates about midway between the soma and the apical tuft has these measurements
oc>dend11[22] print L, diam
398.28092 4.3886497
but after that neurite's "folding factor" is applied
oc>dend11[22] print L,diam
414.09084 5.058138
"I can live with that."
Maybe, but you have to realize that the contribution of spines to surface area has already been "baked into" the model, and you better be happy with the particular spine area contribution that they used.
For some time now, most modelers who are creating model cells based on detailed morphometric data aren't using the "folding factor" approach. Instead they're just multiplying specific membrane capacitance and channel densities by a factor that represents the fractional increase of surface area. Example: if you assume that a particular neurite's spine density is 1 spine/um2 and that average spine surface area is 1 um2, the effective total surface area of that neurite will be twice as large as one would calculate from L and diam (or the pt3d data), so multiply that section's cm and channel densities by 2.
If on the other hand you assume that spine density is best described in terms of spines per um length, the relative contribution of spines to surface area will depend on local neurite diameter.
area of a 1 um length of bare neurite with diameter diam = PI*diam
So if there is 1 spine/um, and average spine area is 1 um2, the total area of a 1 um length of neurite is 1 + PI*diam, so spines increase neurite area by the factor (1 + PI*diam)/(PI*diam) = 1 + 1/(PI*diam). This means that, after nseg has been specified, one must iterate over all dendrites (soma too if the same rule applies to soma membrane) and apply the appropriate factor to all density parameters. Example: assuming that the soma and dendrites all have spines, and have all been appended to a SectionList called spiny, one would
forsec spiny for (x,0) { // iterate over internal nodes only
factor = 1+1/(PI*diam(x))
cm(x) *= factor
gbar_naf(x) *= factor // assuming that mechanism with suffixes naf and kdr have been inserted
gbar_kdr(x) *= factor
. . . etc. . . .
}
To me, it makes more sense that spine density should be specified as spines per unit area, not per unit length.
Fortunately the source code for their model contains all of the original morphologies, free of any "corrections". Use NEURON to execute one of the hoc files in the cells subdirectory; the code for the L5 pyramid is in j4a.hoc, and it creates a model that imports nicely into the CellBuilder.
I started setting the biophysics with the Biophysics tab following these instructions
http://www.neuron.yale.edu/neuron/stati ... ophys.html. Unfortunately, I'm being asked to enter the parameters for all 176 sections individually. Is there a way around this?
For example, in the code all the dend sections are in the list 'dendritic', so parameter values for all dend section can be set with "forsec dendritic". Is there a way to do something similar in CellBuilder->Biophysics?
An important question. In your excitement (or fatigue), you may have skipped over the part of the CellBuilder tutorial that addresses how to define subsets. It's step 2 in that tutorial.
And if you want to specify that some parameter varies systematically over the cell, e.g. as a function of distance from the soma, you'll want to look at the CellBuilder tutorial about
"Specifying parameterized variation of biophysical properties"--see
http://www.neuron.yale.edu/neuron/stati ... /main.html