Search found 41 matches

by sgratiy
Tue Apr 03, 2012 5:19 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Ca-activated K-current with dynamic [Ca]_i clamp
Replies: 4
Views: 2431

Re: Ca-activated K-current with dynamic [Ca]_i clamp

Thanks Ted, your suggestions are very helpful. Now I understand how Vector's play method works.
by sgratiy
Fri Mar 30, 2012 7:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Ca-activated K-current with dynamic [Ca]_i clamp
Replies: 4
Views: 2431

Re: Ca-activated K-current with dynamic [Ca]_i clamp

Ted, thanks for a speedy response. Do I understand correctly that using Vector's play method is preferred when using the variable time step? Also, assuming that I only care about [Ca]_i in the soma and assuming that at each point in time the somatic [Ca]_i is uniform, is this the correct way of assi...
by sgratiy
Thu Mar 29, 2012 8:12 pm
Forum: Getting started
Topic: Exporting vectors to .dat file afte each time step
Replies: 5
Views: 3506

Exporting vectors to .dat file afte each time step

I need to be able to export the spatial CSD vector at each time step to the external file for plotting with Matlab. I implemented the solution, but wanted to ask for the feedback on whether or not this is the optimal way of doing this. The CSD vector is calculated at each time step with the update_c...
by sgratiy
Thu Mar 29, 2012 3:10 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modeling dynamic extracellular fields
Replies: 19
Views: 9625

Re: Modeling dynamic extracellular fields

I thought that simply inserting the existing extracellular mechanism should take care of an additional current caused by changing vext without a need to modify the hh mechanism, but I may be incorrect.
by sgratiy
Wed Mar 28, 2012 8:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Ca-activated K-current with dynamic [Ca]_i clamp
Replies: 4
Views: 2431

Ca-activated K-current with dynamic [Ca]_i clamp

I need to insert the distributed mechanism for modeling the Ca-activated K-current; more precisely, I am interested in inserting the SK channels into membrane in order to model the medium afterhyperpolarization. In the Sec. 9.6 of the Neuron book I found a relevant example for specifying such a mech...
by sgratiy
Thu Jul 08, 2010 9:45 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 13529

SWC files with a single "soma" point

Some cells from Neuromorpho.org have somata containing only a single 3d point. Even though NEURON's Import3d tool attempts to fix the problem by assigning one of the adjacent points to soma, the information about soma's morphology is greatly compromised for those cells. What strategy would you recom...
by sgratiy
Tue Jul 06, 2010 5:54 pm
Forum: Anatomically detailed models
Topic: Dealing with z-axis jitter in reconstructed cells
Replies: 1
Views: 2001

Dealing with z-axis jitter in reconstructed cells

Some of the cells from NeuroMorpho.org manifest z-axis jitter. This artifact can add quite a bit extra cable length to each cell. As far as I remember from Neuron course, this artifact is caused by the fact that gears on experimental set up are not connecting perfectly, and therefore allow to turn s...
by sgratiy
Wed Jun 30, 2010 7:06 pm
Forum: Getting started
Topic: Movie Run for a user defined array
Replies: 6
Views: 2477

Re: Movie Run for a user defined array

Yes, this is a mean field calculation, because it assumes that we calculate the CSD from an entire population of identical cells distributed along a cortical layer with some density, rather than from a single cell.

Thanks,
Sergey
by sgratiy
Wed Jun 30, 2010 5:31 pm
Forum: Getting started
Topic: Movie Run for a user defined array
Replies: 6
Views: 2477

Re: Movie Run for a user defined array

Ted, I followed your suggestion and implemented graphs via hoc statements. Also, thanks for pointing out the Matrix class for me. I have now implemented my code using strictly Vector and Matrix classes. However, I have a minor problem: The description of Graph class states that when using .plot func...
by sgratiy
Mon Jun 28, 2010 9:27 pm
Forum: Getting started
Topic: Movie Run for a user defined array
Replies: 6
Views: 2477

Re: Movie Run for a user defined array

Ted, thanks it worked. However, I have some issues with saving this window into a session file for reuse. The first time I execute my code with a custom advance() procedure I created the graph using 'g = new Graph()' statement. Then, I saved my session which included a plot of 'csdvec' into a .ses f...
by sgratiy
Fri Jun 25, 2010 11:42 pm
Forum: Getting started
Topic: Movie Run for a user defined array
Replies: 6
Views: 2477

Movie Run for a user defined array

I need to be able to plot an array whose values change as a function of time during the simulation using Movie Run. In the code below an array in question 'csdvec' is a linear transformation of i_membrane(x). Currently, I run the simulation for a certain duration of time and then reexecute the code ...