Search found 5677 matches

by ted
Tue Jan 28, 2020 12:43 pm
Forum: NEURON hacks
Topic: How to connect multiple compartments of an axon using a for loop?
Replies: 3
Views: 19

Re: How to connect multiple compartments of an axon using a for loop?

For some reason, it isn't showing here that there is an i in square brackets next to the axon_1(0). Why don't you use the Forum's markup features? Those little buttons above the big edit field include one that is used to wrap blocks of code. Maybe read about this in the Forum's FAQ list, under "For...
by ted
Tue Jan 28, 2020 12:39 pm
Forum: NEURON hacks
Topic: How to connect multiple compartments of an axon using a for loop?
Replies: 3
Views: 19

Re: How to connect multiple compartments of an axon using a for loop?

Could anyone help me debug this part of my code?
Do you think the task might be simpler if you used a million "compartments" (sections, actually)? Or maybe it would be easier to figure out what went wrong if you tried just 3.
by ted
Tue Jan 28, 2020 12:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling leaky integrate-and-fire neuron including Hodgkin–Huxley-like currents
Replies: 1
Views: 24

Re: Modeling leaky integrate-and-fire neuron including Hodgkin–Huxley-like currents

1. Is my implementation correct? How will you discover whether it works properly? Did Esser et al. publish a figure that shows how one of their model cells responds to injected current or synaptic activation? Or is such a figure in their previous paper that they cited as the basis for this model? I...
by ted
Tue Jan 28, 2020 11:15 am
Forum: NEURON + Python
Topic: Rset or reboot neuron without exist in python
Replies: 3
Views: 804

Re: Rset or reboot neuron without exist in python

So is there a method to fully reset the simulator? Yes. It's called finitialize(), and it takes care of everything that is built into NEURON. But if you write some code that adds new state variables, it's up to you to make sure that those new state variables are properly initialized. See my previou...
by ted
Fri Jan 24, 2020 11:34 am
Forum: Parallel NEURON
Topic: multiple signals to a single POINT_PROCESS and thread safety of a POINTER.
Replies: 1
Views: 42

Re: multiple signals to a single POINT_PROCESS and thread safety of a POINTER.

How about approching the problem in a way that completely eliminates the need for pointers? The strategy depends on whether dopaminergic modulation of plasticity is stream-specific (selectively affects individual synapses) or not stream-specific (e.g. mediated by an intracellular second messenger th...
by ted
Tue Jan 14, 2020 9:17 pm
Forum: Modeling networks
Topic: design afferent stimulus events with phasic bursts
Replies: 3
Views: 69

Re: design afferent stimulus events with phasic bursts

. . . if I need to deliver . . .
So? Have you tried to do it? How do you know there is a problem if you haven't tried it?
by ted
Tue Jan 14, 2020 11:45 am
Forum: Modeling networks
Topic: design afferent stimulus events with phasic bursts
Replies: 3
Views: 69

Re: design afferent stimulus events with phasic bursts

If for each burst with specific intra-burst freq, I design a netstim() for it, that would be ending up with too many netstim() Really? What operating system are you using, and how much memory does it have? Assuming your code allows you to specify how many cells the network has, what is the largest ...
by ted
Mon Jan 13, 2020 1:00 pm
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 53

Re: Finding middle of a section

h.define_shape() does not create new points for sections whose morphology was defined by calling the pt3dadd method. True. My mistake. The way to discover the xyz locations of segment centers is to treat a section's pt3d data as piecewise linear functions of path length from the section's 0 end, an...
by ted
Mon Jan 13, 2020 11:40 am
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 53

Re: Finding middle of a section

I am currently working on an algorithm for finding the min. current needed to produce an action potential using extracellular stimulation and the MRG axon You say nothing about the geometry of the stimulating electrode(s) (point electrodes vs. electrodes with finite surface area, monopolar vs. bipo...
by ted
Mon Jan 06, 2020 8:26 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding cilia with an added mechanism to a dendrite
Replies: 2
Views: 78

Re: Adding cilia with an added mechanism to a dendrite

You may be the only person on the planet who knows what you are asking. Let's see if we can make your question more understandable to others. I have a neuron model with soma, dendrite and cilium. Each of these is represented by a section? The cilium has a mechanism added that gives variation of 8 va...
by ted
Thu Jan 02, 2020 10:05 pm
Forum: NEURON + Python
Topic: Print Issue after using .connect()
Replies: 1
Views: 126

Re: Print Issue after using .connect()

For readers who wonder what came of this-- Diagnosis of this problem was complicated by two facts. First, the user isn't seeing error messages. On a different PC the code produced an error message to the effect that a connect statement failed because it would have connected a section to itself, resu...
by ted
Wed Jan 01, 2020 7:48 pm
Forum: NEURON + Python
Topic: Associative arrays in HOC
Replies: 5
Views: 190

Re: Associative arrays in HOC

As long as Python is installed, you can use Python dictionaries from inside HOC
This looks like the way to go--avoids trying to use hoc to replicate existing Python functionality.
by ted
Wed Jan 01, 2020 2:34 pm
Forum: NEURON + Python
Topic: Converting HOC extracellular to Python
Replies: 3
Views: 109

Re: Converting HOC extracellular to Python

As ramcdougal notes, the hoc statement insert extracellular xraxial=Rpn0 xg=1e10 xc=0 will affect xraxial[0], xg[0], and xc[0] of the currently accessed section. extracellular's "0" layer is the one that is right next to the external surface of the section, and it's usually the one whose parameters ...
by ted
Wed Jan 01, 2020 11:43 am
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 178

Re: replicate Waxman's model

I wonder if I use a finer scale (Δx=10um, n_seg=200, compared with Waxman: Δx=200um, n_seg=10),apply Crank-Nicholson method with an integration time increment Δt=5 us, then I should get a more accurate result, is that right? That's not going to resolve the differences between their results and the ...
by ted
Wed Jan 01, 2020 11:00 am
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 178

Re: replicate Waxman's model

On re-reading Brill et al. 1977 I saw that my interpretation of "internodal conduction time" was incorrect. They define it as "the difference in times at which the rising phase crossed 50 mV at two consecutive nodes." This means that spike time measurement must be made at the centers of two consecut...