www.neuron.yale.edu

Ok nice - and then you would need a `load_json`function, something like: def load_json(morphfile): with open(morphfile, 'r') as f: secdata = json.load(morphfile) seclist = [] for sd in secdata: # make section sec = h.Section(name=sd['name']) seclist.append(sec) # make 3d morphology for x,y,z,d in zi...

I have a use case where I import a (large, complex) morphology from an swc file. Then I have a procedure for pruning branches to make a simpler morphology. At the end of the day, I have a python list with of NEURON section objects (they are all connected and the list contains the root node). Now I w...

I'm in the process of making a Dockerfile for NEURON to make it easier for others to try out simulations without installing on their own machines. I anticipate that I'll have a lot of questions throughout the course of this process... Apologies in advance, I haven't installed NEURON on a machine in ...

Yes, I don't need to run the code multiple times within the same iPython session. I just happened to be doing that when I was testing things out... So I have a satisfactory solution to the problem.

I finally figured it out. There is nothing wrong with the code, but NEURON does not clean up after itself, causing the code to crash the second time its run. Before I was doing this: $ ipython In [1]: %run model.py # this works fine the first time In [2]: %run model.py # the second run usually segfa...

So I updated the code to keep the h.Vector() objects in memory. Another post on the forum seemed to suggest that this was important. However, I'm still getting sporadic segfaults. The code DOES work maybe 50% of the time. When I comment out the section for adding synapses, I get no segfaults. from n...

Thanks for the reply. I think I'm moving in the right direction. However, the code below segfaults and I'm not sure why (it may be completely unrelated to the synapses, I will investigate further). from neuron import h import numpy as np import pylab as plt # Load morphology and other stuff h.load_f...

This is a very basic question. I would like to implement a python function that adds an Exp2Syn at a specified location, which triggers a series of post-synaptic events at specified times. I want to do something like: from neuron import h def add_synapse(section,loc,weight,times): " " &quo...

In case anybody is interested, I figured out how you can do this in Python: from neuron import h dend1 = h.Section() dend2 = h.Section() dend3 = h.Section() h.pt3dadd(0,0,0,1,sec=dend1) h.pt3dadd(1,0,0,1,sec=dend1) h.pt3dadd(0,0,0,1,sec=dend3) h.pt3dadd(0,1,0,1,sec=dend3) for s in dend1,dend2,dend3:...

Hi Ted, I'm interested in activity-dependent transcription of mRNA and its transport to neurites. Some mRNAs can be produced and transported quite rapidly (~15 minutes after high frequency stimulation). I like the idea of a phenomenological model, but I would like to couple mRNA production and expre...

I'm curious if it is possible to use the rxd module to model active transport of intracellular solutes. For a simple example, suppose I have two sections: from neuron import h, rxd soma = h.Section() dend = h.Section() dend.connect(soma , 1, 0) Lets say that some mRNA transcript of ('m') interest is...

I have a couple of mechanisms that need to know the surface area of the section they are inserted into. I tried to achieve this by the following code ASSIGNED { diam (um) L (um) surface_area (um) } BREAKPOINT { surface_area = 3.141592 * diam * L } I found that diam was correctly specified... but... ...

Excellent. Thank you!

I am now getting a list of compile-time errors. The first listed one is: invalid storage class for function 'state_change' I get this error for the following code: DERIVATIVE state_change { rates(v) : Calculate minf, taum, hinf, tauh m' = (minf-m)/taum h' = (hinf-h)/tauh if( plastic==1 ){ gbar' = (a...

Great! This is easy to implement. Thanks for your help.

Out of curiousity, how does NEURON handle the line
Will this slow the simulation down a little bit, or is it smart enough to ignore gbar in the integration routine entirely?

Thanks again!