// \$Id: calcrxc_a.hoc,v 1.4 2010/05/10 18:43:19 ted Exp ted \$ /* Calculates the transfer resistances between extracellular stimulating|recording electrode(s) and a model neuron. Relies on the principle of reciprocity, which assumes that the intervening bath and tissue can be treated as linear. Suppose a stimulus current of amplitude Is, applied to a particular configuration of extracellular electrode(s), produces a potential Vext(x,y,z) at location (x,y,z). Then the transfer resistance between the electrode(s) and (x,y,z) is rx(x,y,z) = Vext(x,y,z)/Is According to the principle of reciprocity, a transmembrane current Im(x,y,z) generated by membrane at (x,y,z) will produce a potential Vel that can be recorded at the extracellular electrode(s) and is given by Vel = rx(x,y,z) Im(x,y,z) ----------------------------------------- How to simulate extracellular stimulation ----------------------------------------- Insert the extracellular and xtra mechanisms in all sections that are subject to the extracellular field. Compute the transfer resistance rx for every section that contains xtra, as illustrated below. Construct a stimulus waveform template and copy it to a Vector. For each internal node along the axon, use this Vector to drive is_xtra(x). The xtra mechanism uses the rx values to convert the stimulus current waveform into the proper amplitude and sign of the local extracellular field. If rho, b, or c is changed, new_elec() must be invoked to make the changes take effect. ----------------------------------------- Monopolar electrode in an infinite medium ----------------------------------------- A conductive sphere of radius r0 is suspended in an infinite volume of solution that has resistivity rho [ohm cm]. Ignoring electrochemical effects at the electrode|solution interface, what is the resistance between the surface of the sphere and an infinitely distant ground electrode? The surface area of a sphere with radius r is 4 PI r^2. The resistance of a shell with thickness dr is rho dr / 4 PI r^2 and the resistance is therefore inf INTEGRAL rho dr / 4 PI r^2 r0 inf = - rho / 4 PI r | = rho / 4 PI r0 r0 So to a first approximation, a monopolar stimulating electrode that delivers current I produces a field in which potential V is given by V = I rho / 4 PI r where r is the distance from the center of the electrode. The principle of superposition may be applied to deal with an arbitrary number of monopolar electrodes, or even surface electrodes with different shapes and areas, which are located at arbitrary positions, and deliver arbitrary stimulus currents. However, there are some noteworthy special cases. --------------------------------------------- Special case: bipolar stimulation of an axon --------------------------------------------- Imagine a pair of stimulating electrodes that lie along a line parallel to an axon, like so: ===================== --- c o o --- | b | 1 2 where b is the separation between the electrodes and c is the perpendicular distance from them to the axon. For the sake of this example, assume that the electrodes straddle the midpoint of the axon. The extracellular potential at location x produced by electrode 1 is V1 = I rho / 4 PI r1 where r1 is the distance from electrode 1 to x. This distance is r1 = sqrt( ((x-0.5)*L) + 0.5*b)^2 + c^2 ) Likewise the potential at x produced by electrode 2 is V2 = -I rho / 4 PI r2 where r2 is the distance from electrode 2 to x, i.e. r2 = sqrt( ((x-0.5)*L) - 0.5*b)^2 + c^2 ) The net extracellular potential at x is V1 + V2, i.e. Vnet = (I rho / 4 PI)*((1/r1) - (1/r2)) so the transfer resistance that converts the stimulus current I to an extracellular potential Vnet is simply rx = (rho / 4 PI)*((1/r1) - (1/r2)) -------------------------------------------------------- Special case: uniform field between two parallel plates -------------------------------------------------------- A uniform field has the same intensity and orientation at all points in space, and the extracellular potential at any point is a linear function of displacement in the direction of the orientation of the field. If an entire neuron lies in such a field, then without loss of generality we may assert that the extracellular potential is 0 for all points that lie on some plane that is perpendicular to the field. For this "zero potential surface" it is convenient to choose the plane that passes through a particular location in the cell, such as the 0 end of the soma. */ // set up the transfer resistances // what is the approximate resistivity of tissue anyway? //rho = 35.4 // ohm cm, squid axon cytoplasm // for squid axon, change this to seawater's value rho = 351 // for living mammalian cells, change to brain tissue or Ringer's value 351 from brain resistivity paper /* b = 400 // um between electrodes c = 100 // um between electrodes and axon proc setrx() { forall { if (ismembrane("xtra")) { // avoid nodes at 0 and 1 ends, so as not to override values at internal nodes for (x,0) { r1 = sqrt( ((x-0.5)*L + 0.5*b)^2 + c^2 ) r2 = sqrt( ((x-0.5)*L - 0.5*b)^2 + c^2 ) // 0.01 converts rho's cm to um and ohm to megohm axon.rx_xtra(x) = (rho / 4 / PI)*((1/r1) - (1/r2))*0.01 // print r1, r2 } } } } */ // assume monopolar stimulation and recording // electrode coordinates: // for this test, default location is 50 microns horizontal from the cell's 0,0,0 // BILL: for my model, I have the pyr cells in the yz plane (+/- 205) centered at x=0. The baskets are 10 um deep at x=10 // thus, electrode at x=-50 or -100 or -500 would be best. These need to be called outside this function in setelec(-50, 0 ,0) XE = -50 // um YE = 0 ZE = 0 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 //print secname(), " \t", rx_xtra(x) } } } } proc setelec() { xe = \$1 ye = \$2 ze = \$3 setrx(xe, ye, ze) } /* 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) pt3dadd(\$1+0.5, \$2, \$3, 1) pElec = new IClamp(0.5) } gElec.point_mark(pElec, 2) // make it red } proc setelec() { xe = \$1 ye = \$2 ze = \$3 setrx(xe, ye, ze) //drawelec(xe, ye, ze) } // setrx(50, 0, 0) // put stim electrode at (x, y, z) setelec(XE, YE, ZE) // put stim electrode at (x, y, z) // print "Use setelec(x, y, z) to change location of extracellular recording electrode" xpanel("Extracellular Electrode Location", 0) xlabel("xyz coords in um") xvalue("x", "XE", 1, "setelec(XE,YE,ZE)", 0, 1) xvalue("y", "YE", 1, "setelec(XE,YE,ZE)", 0, 1) xvalue("z", "ZE", 1, "setelec(XE,YE,ZE)", 0, 1) xpanel(855,204) */