graphs in extracelllular stimulation

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ted
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Re: graphs in extracelllular stimulation

Post by ted » Fri Jul 19, 2013 3:47 pm

shwetakgp wrote:the values of conductances of the ion channels which are already present in the cell builder, are they the default values of the conductance???
They are the default vaules specified in the NMODL files that define the channels' properties. Many models use values that differ from the defaults, so if you're using a model you found in ModelDB, I'd suggest using ModelView to check the actual values that were used.
if i use those values do i have to mention any reference
If you are using channels from a published model, it is a good idea to cite the paper that described the model. If you got your NMODL files from ModelDB, the model entry in ModelDB should contain a citation of the paper.
what should be the value to max conductance if conductance is say 70 ms/ohm2
Units for a density mechanism (like any ordinary voltage gated current whose channels are distributed over the surface of a cell) should generally be in Siemens per cm2. Actual conductance for any particular channel is usually calculated as a product of a "conductance density parameter" in S/cm2 times one or more gating variables, each of which lies between 0 and 1. The product of the gating variables is the "open fraction" (fraction of channels that are in the open state).

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Fri Jul 19, 2013 5:08 pm

i am using xtra.mod from the extracellular stimulation and recording.zip. so what reference should i mention and how?

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Re: graphs in extracelllular stimulation

Post by ted » Fri Jul 19, 2013 10:12 pm

For xtra.mod and the other files in extracellular_stim_and_rec.zip, I'd suggest a citation like this:

xtra.mod and other files from extracellular_stim_and_rec.zip, by N.T. Carnevale, downloaded as
http://www.neuron.yale.edu/ftp/ted/neur ... nd_rec.zip
on << whatever date you downloaded them >>

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Tue Aug 06, 2013 9:16 am

dear ted,
my axon has the same value of threshold current but it shows a spike 6 to 7 seconds after the spike of soma. is this okey?

and for making a disc electrode do i need morphometric data of the neuron or a three dimensional model of the neuron??

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Re: graphs in extracelllular stimulation

Post by ted » Tue Aug 06, 2013 10:16 pm

shwetakgp wrote:it shows a spike 6 to 7 seconds after the spike of soma. is this okey?
Seconds, not milliseconds? And where in the axon is this spike observed?
for making a disc electrode do i need morphometric data of the neuron or a three dimensional model of the neuron??
You need to know the extracellular potential as a function of location in space. How you calculate that is up to you.

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Sun Aug 11, 2013 3:18 pm

sorry my mistake , milliseconds . is it ok for axon and soma to have same threshold current value ???
i mentioned this earlier too... could i do this way:
To make a disc electrode i thought that i should start with a point and take a current density sigma. taking the point, i can assume a disc of radius r.
for calculating the current i could integrate it taking a ring of thickness dr as the element of integration. Then multiplying the area found by the current density could give me the current provided by the disc. let me know if this is feasible

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Thu Aug 15, 2013 10:33 am

dear ted,
please reply to my query and let me know if making a disc electrode that way could work

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Re: graphs in extracelllular stimulation

Post by ted » Thu Aug 15, 2013 11:37 am

shwetakgp wrote:sorry my mistake , milliseconds . is it ok for axon and soma to have same threshold current value ???
Depends on the model cell. Also, depending on the shape of the cell and the distribution of ion channels, if you're injecting a current at some point A, the action potential might really arise at some other point B.
i mentioned this earlier too... could i do this way:
To make a disc electrode i thought that i should start with a point and take a current density sigma. taking the point, i can assume a disc of radius r.
for calculating the current i could integrate it taking a ring of thickness dr as the element of integration. Then multiplying the area found by the current density could give me the current provided by the disc. let me know if this is feasible
Yes, but you need to do that outside of NEURON. Presumably you would get an analytic expression that describes the field as a function of angular displacement from the axis of the disc and euclidean distance from the center of the disc.

What to do with that? If the diameter of the cell's dendritic field is small compared to its distance from the electrode, you could assume that the extracellular potential is uniform across the outer surface of the cell's dendrites. The part of the axon that runs across the retina from the cell to the head of the optic nerve might have some variation of extracellular potential along its length. However, I suspect that the greatest variation of the field will be along the axon after it enters the optic nerve and extends away from the electrode. It would probably be reasonable to assume that the optic nerve travels close to the axis of the disc.

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Sun Aug 18, 2013 3:28 pm

i got an expression of current using a charge density sigma, resistivity rho, diameter and distance of electrode from center of soma.
should i put this current equal to is_xtra as the current from the expression equals to stimulating current produced by the electrode????????? in case of point electrode in calcrxc.hoc we describe its shape in 3-d system. how should i do it for a disc??

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Mon Aug 19, 2013 2:15 pm

how is this for a start ....i made changes in calcrxc.hoc. I is the stimulating current emitted by the elctrode. The analytical fromula of the current through electorde has been derived from simple current electricity equations of electric field for a disc and relation between current density and electric field.
i cant figure out how to describe the shape of a disc electrode, selec() .

Code: Select all

proc setis() {
forall {
if (ismembrane("xtra")) {

Vnet = (I rho / 4 PI)*(1/r)
I = (2σαπa^2)⁄(4πε[ 1- r/(√(r^2+a^2 )  )  ])
// where α is the charge density and a is the radius 
// σ is the conductivity and r is the distance of electrode from soma
{
$1= a
$2= r  } 


proc setrx() {  // now expects xyc coords as arguments
  forall {
    if (ismembrane("xtra")) {
// avoid nodes at 0 and 1 ends, so as not to override values at internal nodes
      for (x,0) {
        r = sqrt((x_xtra(x) - xe)^2 + (y_xtra(x) - ye)^2 + (z_xtra(x) - ze)^2)
//        r = sqrt((x_xtra(x) - $1)^2 + (y_xtra(x) - $2)^2 + (z_xtra(x) - $3)^2)
        // 0.01 converts rho's cm to um and ohm to megohm
        rx_xtra(x) = (rho / 4 / PI)*(1/r)*0.01
      }
    }
  }
}

 create sElec  // bogus section to show extracell stim/rec electrode location
objref pElec  // bogus PointProcess just to show stim location
objref gElec  // will be a Shape that shows extracellular electrode location

gElec = new Shape(0)  // create it but don't map it to the screen yet
// gElec.size(-245.413,275.413,-250,270)
gElec.view(-245.413, -250, 520.827, 520, 629, 104, 201.6, 201.28)

proc drawelec() {
	sElec {
		// make it 1 um long
		pt3dclear()
		pt3dadd($1-0.5, $2, $3, 1) // PROBLEM : HOW TO DESCRIBE THE SHAPE OF THE DISC ELECTRODE
		pt3dadd($1+0.5, $2, $3, 1)
		pElec = new IClamp(0.5)
	}
	gElec.point_mark(pElec, 2)  // make it red
}
 [/quote]

proc setelec() {
	xe = $1
	ye = $2
	ze = $3
        α = $4
	setrx(xe, ye, ze)
	drawelec(xe, ye, ze, α ) // to vary the charge density
}

// setrx(50, 0, 0)  // put stim electrode at (x, y, z)

setelec(XE, YE, ZE, Q)  // put stim electrode at (x, y, z)

xpanel("Extracellular Electrode Location", 0)
  xlabel("xyz coords in um")
  xvalue("x", "XE", 1, "setelec(XE,YE,ZE,Q)", 0, 1)
  xvalue("y", "YE", 1, "setelec(XE,YE,ZE,Q)", 0, 1)
  xvalue("z", "ZE", 1, "setelec(XE,YE,ZE,Q)", 0, 1)
  xvalue("α", "Q",  1, "setelec(XE,YE,ZE,Q)", 0, 1)

xpanel(855,204)

ted
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Re: graphs in extracelllular stimulation

Post by ted » Tue Aug 20, 2013 10:25 am

shwetakgp wrote:The analytical fromula of the current through electorde has been derived from simple current electricity equations of electric field for a disc and relation between current density and electric field.
i cant figure out how to describe the shape of a disc electrode, selec() .
Do you really need a cartoon of the disc? Isn't it enough to show the center of the disc? I suppose, if you know the location of the center of the disc, and also the orientation of its axis, you could draw a set of radii from the disc center, orthogonal to its axis, at regular angular intervals. This could cause a problem if the disc is much larger than the dendritic extent of the cell--you'd have this giant thing that looks like a large, flattened umbrella, and the cell might look like a tiny tangle of lint by comparison.

But suppose you still wanted to do this. Something like this would work:

Change
create sElec // bogus section to show extracell stim/rec electrode location
to
NUMELEC = 4 // or 6 or however many radii you want to draw
create sElec[NUMELEC] // bogus sections to show extracell stim/rec electrode location

Change drawelec() to

Code: Select all

// first 3 arguments are the x, y, and z coords of the center of the electrode in microns
// which of course will be the starting point for all of the sElec sections
// 4th argument is the electrode radius in centimeters

proc drawelec() { local i, rad, xx, yy, zz
  rad = $4 * 1e4 // rad is radius in um
  for i=0,NUMELEC-1 {
    . . . given the orientation of the electrode's axis,
          calculate angular orientation of this radius section . . .
    . . . knowing its angular orientation, and its length in um, 
          calculate the coordinates (xx, yy, zz) of its end point . . .
    sElec[i] {
      pt3dclear()
      pt3dadd($1, $2, $3, 1) // 
      pt3dadd($1+xx, $2+yy, $3+zz, 1)
    }
  }
  // attach an IClamp to the origin of the first sElec section
  sElec[0] pElec = new IClamp(0.5)
  gElec.point_mark(pElec, 2)  // make it red
}
where obviously I have left out the calculation of the orientation and end point of each radius section.

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Tue Aug 20, 2013 2:17 pm

i wanted to create a disc electrode because i have to compare my results with experimental results and practically i cant assume elctrode to be a point electrode. Is there any way i could create an electrode with dimensions and vary its dimensions( which, for the disc i thought to be radius) to see the effect on the reponse of the neuron. If not then about your previous query i have chosen the axis to be perpendicular to the plane of the cell. can i take any angular orientation?????
and then calculate arc length by multiplying radius with angular orientation( L= r*theta). for the end point y and z coordiantes could be zero and x coordiante equal to radius??

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Re: graphs in extracelllular stimulation

Post by shwetakgp » Wed Aug 21, 2013 2:36 pm

please reply to my previous query .
i was studying about myelinated axon and couldnt understand some things-
Ra=rhoa*(1/(paraD1/fiberD)^2)/10000
cm=2*paraD1/fiberD
insert pas
g_pas=0.001*paraD1/fiberD
e_pas=v_init
insert extracellular xraxial=Rpn1 xg=mygm/(nl*2) xc=mycm/(nl*2)
how have these terms been calculated?
what are paranodes1 and 2 and what is meant by this term space_p1=0.00 and how nodes have been connected

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Re: graphs in extracelllular stimulation

Post by ted » Wed Aug 21, 2013 9:40 pm

shwetakgp wrote:Is there any way i could create an electrode with dimensions and vary its dimensions
No.
If not then about your previous query i have chosen the axis to be perpendicular to the plane of the cell. can i take any angular orientation
What angular orientation do you mean? You have the coordinates of the cell's sections so you know the plane in which the cell lies. You also know the orientation of the plane in which your disc electrode lies.

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Re: graphs in extracelllular stimulation

Post by ted » Wed Aug 21, 2013 9:43 pm

shwetakgp wrote:please reply to my previous query .
Done.
i was studying about myelinated axon and couldnt understand some things
This question is way off the topic of the remainder of this thread. If you want to post it on the forum, please open a new discussion thread and keep that thread focused on the topic of myelinated axons.

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