Search found 5673 matches

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: 22

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: 61

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: 61

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: 47

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: 47

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: 75

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: 118

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: 185

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: 103

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: 169

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: 169

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...
by ted
Tue Dec 31, 2019 2:51 pm
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 169

Re: replicate Waxman's model

First let me apologize for this delayed reply. I've zipped my file (for the first two figures)and sent to your email I received your email message, but it had no attachment. Try again? The model used by Waxman et al. 1978 is based on what they used for Brill, Waxman, Moore, and Joyner (1977) Conduct...
by ted
Sun Dec 22, 2019 9:36 pm
Forum: Anatomically detailed models
Topic: altering length and diameter over a subset
Replies: 1
Views: 131

Re: altering length and diameter over a subset

for i=1, 8 {
forsec all_dendrite {L=L/i} <--- you changed the length of every section in "all_dendrite"

forsec all { nseg = int((L/(0.1*lambda_f(100))+.999)/2)*2 + 1 } <--- now you're changing nseg in every section in "all"
...

analysis()
}
by ted
Sun Dec 22, 2019 9:29 pm
Forum: Suggestions and Feedback
Topic: Accessibility of documentation
Replies: 1
Views: 113

Re: Accessibility of documentation

Fixed on Friday.

--Ted
by ted
Wed Dec 18, 2019 9:10 pm
Forum: Anatomically detailed models
Topic: Is there any way to bifurcate axon?
Replies: 3
Views: 124

Re: Is there any way to bifurcate axon?

That ModelDB entry actually contains several models. One is very simple (defined by demofig2.hoc)--uses two compartments to represent the entire cell. This is probably not the model that you mean. The other models are based on anatomical data from real cells. However, none of that data includes any ...