Search found 31 matches

by Meena
Wed Oct 03, 2007 6:12 pm
Forum: Getting started
Topic: Classical Cable Theory
Replies: 3
Views: 7988

Classical Cable Theory

Hi! I was just looking at the paper: http://www.neuron.yale.edu/neuron/papers/NIPS94/nipsfin.html I have a question on defining electrotonic distance in the classical cable theory and in NEURON. 1. When we say electrotonic distance do we mean the distance at which the voltage has reduced to 1/e of i...
by Meena
Thu Sep 13, 2007 10:08 am
Forum: Getting started
Topic: d_lambda rule
Replies: 1
Views: 2835

d_lambda rule

Hi, I have some questions regarding how nseg is determined in NEURON to achieve the best possible accuracy. Some of my questions maybe be basic, but please bear with me. I know from reading the textbook that the d_lambda rule can be used to determine the optimal nseg number. (Page 122). The first fe...
by Meena
Tue Sep 04, 2007 2:18 pm
Forum: Getting started
Topic: Questions on Internal Nodes
Replies: 1
Views: 2240

Questions on Internal Nodes

Hi, I am modelling a soma with nseg=1 and a dendrite with nseg=2. I know from reading the neuron textbook that the nseg governs how the internals nodes are placed. Let's also assume that the soma and dendrites in my model are represented by simple RC circuits. (i)Since the soma has nseg=1, the nodes...
by Meena
Sat Jun 23, 2007 7:28 pm
Forum: Getting started
Topic: Neurolucida Tracing
Replies: 0
Views: 3476

Neurolucida Tracing

Hi, I am working on putting together a small document on good tracing techniques and considerations when tracing a cell using Neurolucida. From my reading so far, there is a lot of emphasis on good microscope setup and calibration. Also, there is much stress of the need for shrinkage correction to o...
by Meena
Fri May 18, 2007 9:30 am
Forum: Getting started
Topic: Undefined symbol _nrnmpi_myid referenced from nrnmech.dll
Replies: 2
Views: 3002

Hi again,

I tried deleting nrnmech.dll and any .c and .o files, then running mknrndll,
but that did not work.

I ended up having to remove Neuron and re-installing it but that worked!!!

Thanks so much!
Meena
by Meena
Fri May 11, 2007 11:13 am
Forum: Getting started
Topic: Undefined symbol _nrnmpi_myid referenced from nrnmech.dll
Replies: 2
Views: 3002

Undefined symbol _nrnmpi_myid referenced from nrnmech.dll

Hi, I have Neuron 5.9 already installed in my personal computer - everything runs and works fine. But when I tried installing Neuron 5.9 into another machine and running my files from here, I am prompted with this error: loading membrane mechanisms from nrnmech.dll Undefined symbol _nrnmpi_myid refe...
by Meena
Wed Mar 28, 2007 3:50 pm
Forum: Anatomically detailed models
Topic: Modelling soma as 3D vs a cylindrical section
Replies: 7
Views: 8874

Modelling soma as 3D vs a cylindrical section

Hi Ted, <html>How? Using the Import3D tool? </html> Yes, I used the Import 3D tool <html>Meaning you do exactly what?</html> The first thing I did was to look at the cell in Neurolucida Explorer and find the major and minor axis ( I am assuming the soma can be estimated using a prolate shperoid). Th...
by Meena
Mon Mar 26, 2007 3:57 pm
Forum: Anatomically detailed models
Topic: Modelling soma as 3D vs a cylindrical section
Replies: 7
Views: 8874

Modelling soma as 3D vs a cylindrical section

Hi, I have a question on modelling the cell as a 3D structure in Neuron vs modelling it as cylindrical section. I received a Neurolucida image of cell soma (in .asc format) and converted this into Neuron. I would like to assume the soma as a prolate spheroid as I think this is a reasonable assumptio...
by Meena
Fri Mar 09, 2007 9:10 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding NaCa and caL to model
Replies: 2
Views: 3416

Hi Ted, Thanks so much but I've looked and looked at it - and found that in my model - (as mentioned I have INaca and ICal and ICap) ica in my model was = ICal - INaca I found this out - by removing one of the currents mech and looking at the ica and the adding the mechanism - as far as adding up go...
by Meena
Mon Mar 05, 2007 6:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding NaCa and caL to model
Replies: 2
Views: 3416

Adding NaCa and caL to model

Hi, I am trying to add two mechanisms that will write ica - the sodium calcium exchanger and the long lasting calcium mechanisms to my model. So the first part of the for the Nacax would look like: SUFFIX naca USEION ca READ cai,cao WRITE ica USEION na READ nai,nao WRITE ina and the first part of th...
by Meena
Fri Jan 26, 2007 3:06 pm
Forum: Getting started
Topic: Question about saving current data
Replies: 3
Views: 3990

Thanks for the pointer Ted & Raj,

It works fine now and I managed to save the data that I was infact hoping to save!
by Meena
Wed Jan 17, 2007 12:42 pm
Forum: Getting started
Topic: Question about saving current data
Replies: 3
Views: 3990

Question about saving current data

Hi, I am trying to save the sodium current at the soma in my model in an .asc file. This current would be called soma.i_na(0.5) When I try getting the current profile in Neuron's "current" graph, I have no problem, I see a very small negative ( inward current) on my screen, this is what I expect to ...
by Meena
Fri Dec 08, 2006 10:34 am
Forum: Getting started
Topic: Effective Membrane Resistance
Replies: 12
Views: 21374

Effective Membrane Resistance

Hi again Ted, Ok, so first thing I did now is to move the point of current injection and voltage measure to the "0" The Vm measured was 50.39mV. The RN is (50.39mV+70mV)/1nA=120.39 Mohm. I guess I have much higher value here than when i injected the current and measured the voltage at the center of ...
by Meena
Thu Dec 07, 2006 11:24 am
Forum: Getting started
Topic: Effective Membrane Resistance
Replies: 12
Views: 21374

Effective Membrane Resistance

Hi Ted, I tried this and I am going to take a stab at explanaining it... This cable has surface area of 3143.57 um^2=3.143e-05 cm^2 Setting a g_pas=0.001 S/cm^2 for this structures, implies that the Rm would be 1k ohm.cm^2, or RM = 31.82 Mohm. Applying a current clamp of 1nA for 50ms resulting the V...
by Meena
Wed Dec 06, 2006 2:17 pm
Forum: Getting started
Topic: Effective Membrane Resistance
Replies: 12
Views: 21374

Effective Membrane Resistance

Hi again! Lets say I am trying to investigate the effect of the different holding voltages in a neuron having an active soma and passive dendrites. I control the holding voltage by adjusting the background currents in the model. Can I subject the model to a current clamp, and the look at the voltage...