Search found 104 matches

by shailesh
Thu Mar 19, 2015 1:01 pm
Forum: Other questions
Topic: Regarding connection to ground under extracellular
Replies: 7
Views: 3272

Re: Regarding connection to ground under extracellular

I believe I got that conversion correct in my HOC code with the statement:

Code: Select all

xraxial[0] = ((Ra / ratio_Ra_by_Re)/(PI*((diam*1e-4/2)^2))) * 1e-6
To verify (with pas instead of hh and ratio_Ra_by_Re=1):
xraxial[0]*L*1e-4/nseg = 1.2729849
ri(0.9999) = 1.2729849

So not sure where I have faltered.
by shailesh
Thu Mar 19, 2015 9:36 am
Forum: Other questions
Topic: Regarding connection to ground under extracellular
Replies: 7
Views: 3272

Re: Regarding connection to ground under extracellular

Thanks for suggesting to apply the voltage-divider rule. That cleared a lot of questions. To ease things further I replaced the HH with pas and then observed the plots for vint, vext, vm and i_membrane... and then the picture began to emerge. All the intermediate segments had their vint and vext equ...
by shailesh
Wed Mar 18, 2015 7:09 am
Forum: Other questions
Topic: Regarding connection to ground under extracellular
Replies: 7
Views: 3272

Regarding connection to ground under extracellular

Hi, I again have some query regarding the use of extracellular. I am trying to model a long axon having hh and extracellular mechanism with the connection to ground available at only at one of the terminals (say 1-end). The other end (0-end) of the axon is stimulated via IClamp and I keep track of t...
by shailesh
Thu Jul 03, 2014 11:03 am
Forum: Modeling networks
Topic: Initializing multiple cells using a single cell state file
Replies: 3
Views: 6556

Re: Initializing multiple cells using a single cell state fi

azylbertal... if you still require the above functionality, you could try out this tool here:
https://senselab.med.yale.edu/simtooldb ... ool=155716
(URL updated)

Do let me know if it works out or if you face any issues. Cheers!
by shailesh
Thu Jul 03, 2014 1:07 am
Forum: Other questions
Topic: Issue when updating nseg via custom init()
Replies: 4
Views: 2306

Re: Issue when updating nseg via custom init()

Thanks, that explains it. I was a bit perplexed as I didn't see it coming and found the issue arising when I changed nseg as (nseg=5; nseg<=51; nseg+=2) but not when (nseg=51; nseg>=5; nseg-=2). Not I can see that in the former case, the location of the initial first node might have been drifting to...
by shailesh
Tue Jul 01, 2014 8:27 am
Forum: Modeling networks
Topic: Initializing multiple cells using a single cell state file
Replies: 3
Views: 6556

Re: Initializing multiple cells using a single cell state fi

One of the advantages of the NEURON forum is to randomly go through posts and pickup tips and tricks from others experience! Recently came across this post and my curiosity was piqued reading about SaveState. I was previously unaware of such a feature in NEURON and now realize that it has a lot of p...
by shailesh
Sat Jun 21, 2014 7:36 am
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 9557

Re: Setting Resting Membrane Potential

Thanks for confirming that... an year back when I employed this approach I confess that I did not give it much thought and didn't think of it as a limitation in my model that I could first try working out a solution for by tweaking my channel properties... and if I didn't succeed then resort to such...
by shailesh
Sat Jun 21, 2014 7:18 am
Forum: Optimization
Topic: Regarding fitting of data sampled at irregular intervals
Replies: 11
Views: 10351

Re: Regarding fitting of data sampled at irregular intervals

Thanks. I agree, it would be best to get the raw data (whenever available) for such purposes.
by shailesh
Sat Jun 21, 2014 7:12 am
Forum: Other questions
Topic: Issue when updating nseg via custom init()
Replies: 4
Views: 2306

Re: Issue when updating nseg via custom init()

I am just surprised that changing nseg affected the recording of time 't' which I believe is independent of the number of compartments in a model. I could have expected the voltage vector to spring a surprise because of the change in system equations, but interestingly it records properly with the c...
by shailesh
Fri Jun 20, 2014 5:38 am
Forum: Other questions
Topic: Issue when updating nseg via custom init()
Replies: 4
Views: 2306

Issue when updating nseg via custom init()

Issue when updating nseg via custom init() I was trying to test my model for certain calculated parameters with various values of nseg. The calculations required me to record voltage as well as time using vectors. It seemed appropriate to implement such an exercise using loops. But I encountered som...
by shailesh
Thu Jun 19, 2014 9:06 am
Forum: Other questions
Topic: Setting Resting Membrane Potential
Replies: 14
Views: 9557

Re: Setting Resting Membrane Potential

Had a query regarding the above approach for setting the resting membrane potential by injecting a constant current... ... I was wondering about its physiological meaning. Doesn't it reflect a constant current being injected externally... shouldn't a cell (ideally) be able to maintain its RMP using ...
by shailesh
Thu Jun 19, 2014 8:28 am
Forum: Optimization
Topic: Regarding fitting of data sampled at irregular intervals
Replies: 11
Views: 10351

Re: Regarding fitting of data sampled at irregular intervals

So in context to my first question on this thread: ... does MRF while evaluating the fitness consider only the points provided (loaded from file) or does it implicitly perform a linear interpolation between the data points - and then use all these values for comparison? I suppose we can summarize th...
by shailesh
Wed Jun 18, 2014 2:02 pm
Forum: Optimization
Topic: Regarding fitting of data sampled at irregular intervals
Replies: 11
Views: 10351

Re: Regarding fitting of data sampled at irregular intervals

Based on your comments: the model trajectory is interpolated to the data trajectory and only the resulting values at the data locations are used in the "meansqerr" calculation which is defined as "return value is sum of w *(v1 - v2 )^2 / size". and error is weighted sum of normalized error in each r...
by shailesh
Wed Jun 18, 2014 8:06 am
Forum: Optimization
Topic: Regarding fitting of data sampled at irregular intervals
Replies: 11
Views: 10351

Re: Regarding fitting of data sampled at irregular intervals

Sorry, I wasn't sure what you meant by: ... to make the first comment of this reply, true. and so wanted to clarify. Was it regarding my first question on this thread: 1> If the data (voltage vs time) to be fitted is sampled at irregular intervals, does MRF while evaluating the fitness consider only...
by shailesh
Tue Jun 17, 2014 11:34 pm
Forum: Optimization
Topic: Restricting Parameter Domains
Replies: 2
Views: 7370

Re: Restricting Parameter Domains

Thanks, the workaround you suggested would be good enough for me in this case.

p.s. could I bring your attention to another post that I have not yet been able to resolve:
viewtopic.php?f=23&t=3112#p12897