Code: Select all
spine_dens = 1
spine_area = 0.83
proc add_spines() { local a
forsec dendritic {
a =0
for(x) a=a+area(x)
F = (L*spine_area*spine_dens + a)/a
L = L * F^(2/3)
for(x) diam(x) = diam(x) * F^(1/3)
}
}
Code: Select all
spine_dens = 1
spine_area = 0.83
proc add_spines() { local a
forsec dendritic {
a =0
for(x) a=a+area(x)
F = (L*spine_area*spine_dens + a)/a
L = L * F^(2/3)
for(x) diam(x) = diam(x) * F^(1/3)
}
}
Code: Select all
for(x) a=a+area(x)
Code: Select all
F = (L*spine_area*spine_dens + a)/a
Code: Select all
L = L * F^(2/3)
for(x) diam(x) = diam(x) * F^(1/3)
The approach is explained in the papers written by proponents of anatomical rescaling. Those were published decades ago--early to mid 1980s as I recall. Almost nobody uses that approach any more.charles1 wrote:I have trouble understanding how these two lines of code work
You may call cytoplasmic resistivity Ri, but in NEURON it is called Ra. Ra is unaffected by anatomical rescaling. ri will not be affected if one does anatomical rescaling properly, i.e. scales both length and diameter.2. How does increasing the diameter of dendritic compartments by a factor greater than 1 (F^(1/3)) affect Ri in the dendritic compartments? Ri is defined as the cytoplasmic resistivity of 1 cm^3 of cytoplasm, in units of ohm-cm.
From the specified geometry and Ra. See chapter 5 of The NEURON Book. If you don't have that, seeHow does NEURON compute Ri?