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Dear Ted, Thank you very much for this answer. If I understand properly, all current densities are scaled with segments' dimensions (surface of the segment) and then are incorporated each PP currents. Indeed, sorry for the stupid question, in the doc it's well written: G_syn = weight * factor * (exp...

Dear colleagues, I today started asking myself this simple question "How is point process current added into the equation solved by NEURON". Indeed, from what I understood from the NEURON book, the membrane potential equation solved is typically solved with current density (through distrib...

Thank you very much for the enlightenment on the concept of the AF. Considering the previous example you mentionned, indeed the resolution of the EDP gives (assuming all values to be 1) : Va = 0.5 * exp(-2t) -0.5 -> - 0.5 mV Vb = 0 mV Vc = 0.5 - 0.5exp(-2t) -> 0.5 mV So indeed we can find this linea...

If we take back the circuit associated with the extracellular mechanism (here taken from the previously mentionned post), then we have: Ra o/-- o --\/\/-- o --\/\/-- o --\/\/-- o--\o vext[0] + v intracellular layer | | | | --- --- --- --- | | | | | | c_m = | | g_m --- --- --- --- | | | | | | | | | R...

Dear Ted, Thanks for the reply. Indeed I understand the limitations of the AF. Btw if anybody reads this post, I suggest the following for discussion about this topic and other interesting ones: 10.1016/j.jphysparis.2011.10.003 The limitations are such as only the polarization due to the onset of th...

Dear collegues, I recently took a look at the forum, particularly on these topics: https://www.neuron.yale.edu/phpBB/viewtopic.php?p=18961&hilit=extracellular+math#p18961 and https://www.neuron.yale.edu/phpBB/viewtopic.php?p=19941&hilit=extracellular+equation#p19941, since I am interested in...

Dear colleagues, I used extracellular mechanism with the xtra.mod mechanism to deal with the input. I just found that when I perform the same simulation (same synapses and events) but without extracellular, I don't get the same results (particullarly it seems that the high frequency voltage stimulat...

Finally, I did as explain in the last post using psection() function. The code to save the membrane/mechanisms+ions state was the following (using python) : def save_state(self, fn = None): l = [] for sec in self.cell.all: dic = sec.psection() v = np.array([ seg.v for seg in sec]) l.append( {"v...

Dear Ted, Thank you for your quick feedback. 1. Experimentalists typically wait until v near the spike trigger zone is flat for an amount of time on the order of at least several seconds if not minutes. And even then, they often want each recording to start with at least 1 ms during which that v rem...

Dear all, I am working with pyramidal cell models and my pipeline is pretty simple: Compute steady state of the cell given channel mechanismes ( voltage of all compartments do not vary more than 1e-6 mV from previous step) Preforming my modeling which involve synaptic inputs, calling h.finitialize()...

For those interested by an answer to this issue , I found my way out in changing the default NSTACK and NFRAME via the config NEURON's file. To do so you have to: 1. Going to "nrn/lib/nrn.default" 2. Search for NSTACK (ctrl +f ) 3. On the corresponding line change the value to the desired ...

Dear NEURON team, I am dealing with BBP cells from the 2015 study where they reconstructed a rodent cortical column. I got them from another study on modelDB where the original files are provided (see https://senselab.med.yale.edu/ModelDB/ShowModel?model=241165). I figured out how to use these model...

Dear Ted, As you ask I made a simple ball and stick model to test my extracellular stimulation script. I did a soma (10um x 10um) connected to a dendrite (500 um x 2um) with passive mechanism (Ra =155 O.cm-1, Rm = 17.5 O.cm-2, e_pas=-60 mV) to reproduced the study. Here are my results : https://driv...

Dear Ted, I used a complex model since this is what interest me here to compare with the results of the study I've mentionned. I did figured out how to replicate the results by the way and it involed another way to calculate x,y,z, with some center of mass of the cylinders as I explained in my previ...

Dear Ted, Many thanks for your answer. I did plot RangeVarPlot and as I expected the "e_extracellular" potential is following the trend of the "v" over the soma to apical axis (in the direction of the electric field). It is not linear but It should be due to the fact that apical ...