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Yes, well, I'm new at this deeper stuff, so pardon my inexperience. OK so the general idea is to make dt as small as possible? Obviously much smaller than any time interval (of your curve being fitted). But how much smaller? Is there such a thing as "too small and bad"? For example, if usi...

Hi,

When running the MRF (let's say following tutorials 1 and 2). Curious about the relationship between dt (in RunControl) and the error of Brent's Praxis fitting?

Thanks.
-Charles

Hi Ted,

Thank you for the wonderful, complete answer. I am especially grateful for your suggestion to use worst-case (largest) values for Ra and Cm, if pursuing option 1.

-Charles

Hi,

Curious about how d_lamda is implemented in Cellbuilder. Is the Ra used to compute lamda_f taken from what the user inputs in CellBuilder/biophysics only? Say the user is fitting for Ra at a later stage. Is that Ra taken into account?

I apologize for the lack of clarity. How is what I wish to achieve done? I tried exporting the voltage trace from the voltage axis graph by using "pick vector"; the resolution is very low - not enough voltage points, and no time points. I tried changing dt in the run control menu; the trac...

Hi, I have a morphologically reconstructed cell via a cellbuilder. I wish to create a single test or model pulse of given v_init, delay, amplitude, duration, and total time in Iclamp for this cell. I then wish to download the resultant V(t) vector, in order to model it as per the MRF2 tutorial. Exce...

It's up to you to make sure that whatever changes it makes will affect the model's system equations. Follow a strategy similar to that described in the 2nd MRF tutorial, and cm will end up with whatever value was necessary to satisfy the fit criterion. Say I "spine_scale" g_pas and cm in ...

First, an important point: it works for any compartmental modeling approach or program, not just NEURON. The explanation is pretty straightforward. I really don't know how to make it clearer, except perhaps to use a concrete example. Suppose you have a short piece of neurite with surface area of 10...

A much easier qualitative rationale: Total membrane capacitance and conductance in a compartment are proportional to surface area in that compartment. Using the "apparent" surface area Aa, which is based on neurite diameter and length, gives underestimates of true membrane capacitance and...

Hello, I have trouble understanding how these two lines of code work: L = L * F^(2/3) for(x) diam(x) = diam(x) * F^(1/3) 1. Why does making L longer by a factor of F^(2/3), and making diam(x) bigger by a factor of F^(1/3), add spines to the dendritic section at a density of 1 spine/um, for an indivi...

Hello, Sorry for not mentioning sources explicitly. Here's one; Stuart and Spruston (1998): "Spines were not modeled explicitly, but their effects on membrane area were modeled by decreasing Rm and increasing Cm by a factor of 2 in spiny compartments (Shelton, 1985; Holmes, 1989; Larkman, 1991)...

Hello, It is said that scaling the specific capacitance UP and specific membrane resistivity DOWN in spine-bearing compartments of a model NEURON (layer 5 pyramidal) cell will correct for the absence of the surface area contribution of spines to these compartments (as spines are not seen by Neuroluc...