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I have assumed the cell to experience the propagating electric field as a plane wave (i.e., the potential difference between any points on the plane to which the axis of propagation is orthogonal will be zero). The extracellular potential, I derived using the the formula V_ecm(t) = -E.l_c (from Bosh...

What does NEURON do with extracellular potential 'under the hood'? From the documentation, I took it that NEURON implicitly references both membrane voltage 'v' and extracellular potential 'e' when solving the cable equation, but this gave me unexpected results. When I added the extracellular potent...

The available information on NMODL best practices seems to be contradictory at points, and I wonder if the best current practices could be summarized in one place? As an example, the xtra.mod file states: Prior to NEURON 5.5, the SOLVE statement in the BREAKPOINT block used METHOD cvode_t so that th...

I did get the file online, but it was quite a while ago and I'm not sure of the source. The cell is the layer 5 pyramid from https://www.nature.com/articles/382363a0 , but I had to do some searching to find it. Also, I believe I did some light re-formatting at some point; it's entirely possible I'm ...

I found the issue - bad model data. Just in case anyone else finds themselves with the same behavior, I was using swc data that defined the soma as a single point (in other words, soma_section.n3d()=1). By adding another xyz set to that section, the issue vanished. My guess is that 'extracellular' w...

This may be a long-shot, but I'm hoping I can get some help with a new issue. I've written a Python script to automate cell creation. The script worked perfectly for a cell with Hodgkin-Huxley-like governing equations stimulated by an 'activating function' approach. Now, I'm trying to change to mode...

And one last bit -- I implemented fieldrec() in this way. def fieldrec(v): summa = 0.0 for sec in h.allsec(): for seg in sec: summa += float(seg.xtra.er) v.append(summa) # # later in the code # vrec = [] pyFcall = (fieldrec,vrec) h.CVode().extra_scatter_gather(0,pyFcall) # after which h.finitialize(...

Regarding calc_rxc() -- my understanding is that this function only calculates the resistance of the extracellular medium between the electrode and the neurite segment, and that this value is based on the spatial data from interp_xyz() and is passed on to xtra for calculation of the extracellular po...

I'm going to take these one at a time, starting with interp_xyz() .. I believe the function I posted above is incorrect. I changed the range_var block when I realized I was selecting the edge of the segment, rather than the center . def interp_xyz(section): nn = xr = 0 sec = section #h.cas() # get t...

This issue has kind of sprawled for me as I looked into your suggestions - sorry if the breadth of this post is inappropriate for the forum setting, but hopefully others who are facing the same issues will find this useful. So one thing I realized, as I was going through the read-me associated with ...

I think I'm not implementing the RangeVarPlot correctly; it also shows no activity using the same h.IClamp() instance which successfully excites the cell in a matplotlib graph. Is there additional documentation on RangeVarPlot I can study, if indeed this is the issue?

Thanks for the advice, Ted. Full disclosure: my familiarity with the GUI and the native plotting functions is limited. I made this effort, but the output just flat-lines. So, I'm not sure - is the problem in how I set up the plot, ran the simulation, or implemented the stimulus? # plays a waveform i...

Can anyone help me understand why this code elicits no response in the cell? I've confirmed it's excitable with h.IClamp(), and this code is an adaptation of Ted's from another post. I don't understand the problem. Appreciate it! # plays a waveform into xtra's is from neuron import h, gui from matpl...