/*----------------------------------------------------------------
Geometry file for thalamic reticular neuron
- 8 compartments
- 2 dendrites
Cell from rat nRt, stained by Huguenard & Prince, Stanford [1], and
traced at the Salk Institute by A. Destexhe. Starting from a 80
compartment cell, the geometry was reduced into a simpler geometry
equivalent to dissociated cells. The full and dissociated cells are
depicted in [1].
The dissociated cell was obtained by the following method:
- the full cell has an input capacitance of 69 pF, whereas
dissociated cells have 17.1 pF on average [1].
- if one assumes that the input capacitance is proportional to the
area of the cell, then a typical dissociated cell must have an area of:
14830.5 um2 * 17.1 / 69 = 3675.4 um2
- this area was obtained from the full geometry by keeping the thickest
and most proximal dendrites in order to match this area. The aspect
of the dissociated cell was consistent with the pictures given in [1]
In the dissociated cell, the soma, dend1[0,1,2,3] and dend3[0,1,7] were
kept from the original and renamed soma, dend1[0,1,2,3], and dend2[0,1,2],
repectively. The total membrane area is of 3638.7 um2.
Structure of the reduced compartmental model:
(dend1) 1--0 1--0 1--0 1--0
(dend2) 1--0 1--0 1--0
(soma) 1--0
This model is described in [2]
Alain Destexhe, The Salk Institute, Dec 1994
[1] Huguenard, JR and Prince, DA. A novel T-type current undelies prolonged
calcium-dependent burst firing in GABAergic neurons of rat thalamic
reticular nucleus. J. Neurosci. 12: 3804-3817, 1992.
[2] Destexhe, A., Contreras, D., Steriade, M., Sejnowski, T.J. and
Huguenard, J.R. In vivo, in vitro and computational analysis of
dendritic calcium currents in thalamic reticular neurons.
J. Neurosci. 16: 169-185, 1996.
See also:
http://www.cnl.salk.edu/~alain
http://cns.fmed.ulaval.ca
----------------------------------------------------------------*/
/* make geometry explicit */
primary_branches_cell = 2
branches_cell = 8
nseg_cell = 8
double sections_cell[2]
sections_cell[0] = 4
sections_cell[1] = 3
nsec_cell = 8
strdef name_soma, name_section
name_soma = "soma"
name_section = "dend"
use_axon = 0 /* create sections */
create soma,\
dend1[4],\
dend2[3]
/*----------------------------------------------------------------*/
proc geometry() { local i, j
/* soma geometry */
soma {
nseg = 1
pt3dclear()
for j = 1, fscan() {
pt3dadd(fscan(),fscan(),fscan(),fscan())
}
}
print "soma read"
/* connect primary neurites */
soma connect dend1[0] (0), 0.5
soma connect dend2[0] (0), 0.5
/* neurite geometry*/
for i = 0,3 {
dend1[i] {
nseg = fscan()
pt3dclear()
for j = 1, fscan() {
pt3dadd(fscan(),fscan(),fscan(),fscan())
}
}
}
print "dend1 read"
for i = 0,2 {
dend2[i] {
nseg = fscan()
pt3dclear()
for j = 1, fscan() {
pt3dadd(fscan(),fscan(),fscan(),fscan())
}
}
}
print "dend2 read"
/* branching topology*/
for i = 1,3 {
dend1[fscan()] connect dend1[i] (0), fscan()
}
for i = 1,2 {
dend2[fscan()] connect dend2[i] (0), fscan()
}
}
geometry()
SOMA COORDINATES AND DIAMETERS:
33
-26 1.5 16.5 0
-26 0.75 17.5 2.5
-25.5 1 18 5
-25 0.625 19 8.0039
-24.5 0.25 19 9.8615
-23.5 -0.25 19 11.63
-22.5 -0.5 18.833 12.875
-22 -0.625 18.75 13.521
-20.5 -1.25 18.75 16.14
-18.5 -1.35 18.75 18.263
-18 -1.4375 18.75 18.675
-16.5 -1.5 18.625 19.47
-15 -1.75 18.5 19.906
-14.5 -1.7917 18.5 19.988
-13 -1.9167 20.5 19.833
-12 -2 21 20.025
-11.5 -1.75 21.75 20.555
-10 -1.5 20.75 21.29
-8.5 -1.4375 21 20.519
-8 -1.4167 21 20.233
-7 -1.5 21 19.416
-6 -1.25 20.5 17.755
-5.5 -1.25 20.167 16.714
-4.5 -1.4167 20 15.134
-4 -1.5 19.917 14.354
-3 -1.3333 19.75 12.18
-2.5 -1.375 19.75 10.831
-2 -1.25 20 9.3941
-2 -1.25 21 8.7321
-1.5 -2 22.25 5.0249
-1.5 -1 23 3.6056
-1.5 -0.25 22.5 1.8028
-1.5 0.5 22 0
NEURITE COORDINATES AND DIAMETERS:
1 2
-3 7 -6 7
-5.5 6 -6 7
1 13
-5.5 6 -6 7
-5.5 3.5 -6 6.4
-6 1.5 -6 5.5
-7 -0.5 -6.5 5.3
-8 -2 -7 4.5
-9 -3.5 -7.5 4.3
-10 -5.5 -7 4.3
-11 -7.5 -6.5 4.3
-12 -9 -6 4.3
-13 -11 -6.5 4.3
-14.5 -12.5 -7 4.3
-16.5 -14 -8 4
-18.5 -15.5 -8.5 4.6
1 9
-18.5 -15.5 -8.5 4.6
-20.5 -15.5 -11 3.5
-23 -16 -13 3.5
-24 -17 -16 3.5
-24 -18 -20.5 3.5
-22.5 -19 -25.5 3.5
-22.5 -20.5 -29.5 3.5
-23.5 -21 -32.5 3.5
-25 -22 -35.5 3.5
1 38
-25 -22 -35.5 3.5
-25 -23.5 -33.5 2.9
-25.5 -25 -32.5 2.9
-26 -27 -33 2.9
-27.5 -28.5 -33 2.9
-28.5 -30 -34.5 2.9
-30 -31.5 -35 2.9
-30.5 -33 -36 2
-31 -34 -36.5 2
-31.5 -35.5 -37.5 1.6
-32 -37 -37 1.6
-32.5 -38.5 -37 2
-32.5 -40 -37 2.2
-32.5 -41.5 -37.5 2.2
-32.5 -43 -37.5 2.2
-32.5 -44.5 -36.5 2.2
-32.5 -46 -36 2
-33 -47.5 -35.5 1.6
-33 -49 -35 2.2
-33 -50.5 -35 2.2
-33.5 -52 -35.5 2.2
-33.5 -54 -36 2.2
-33.5 -55.5 -35 2.2
-33.5 -57.5 -34.5 2.2
-33.5 -59 -34 1.7
-33 -60.5 -34 2
-32.5 -62.5 -34 2.2
-31 -64.5 -34 2.2
-29.5 -66 -34 2.2
-28 -68 -34 2.2
-27 -69 -34 2.2
-26 -70.5 -34 2.2
-25 -72 -34 2.2
-24 -73.5 -34.5 1.7
-23 -75 -35 1.7
-22 -76.5 -35.5 1.7
-21.5 -78.5 -35.5 2.4
-21.5 -80 -35.5 3.7
1 19
-25.5 -1 19.5 4.5
-27.5 -1 19.5 3.2
-30 -1 19.5 3.2
-32 -1 19.5 2.7
-34.5 -0.5 19.5 2.7
-36.5 -0.5 19.5 2.7
-38.5 -0.5 18.5 2.4
-40 -0.5 17.5 2.4
-42 -1 16.5 2.4
-43.5 -1 16 3.2
-45 -1 15.5 3
-46.5 -1.5 15 2.5
-48 -1.5 14 2.5
-49.5 -1.5 13.5 2.5
-51.5 -1.5 13 2.5
-53 -1.5 12.5 2.2
-54.5 -1.5 13 2.2
-55.5 -2 15 2.2
-57 -2.5 17.5 2.2
1 35
-57 -2.5 17.5 2.2
-58.5 -2.5 14 1.7
-60 -3 12.5 1.7
-61.5 -3.5 13 1.7
-63 -4 13.5 1.7
-64.5 -4 14 1.7
-66 -4.5 14 1.7
-68 -4.5 14 1.7
-69.5 -4.5 14 1.7
-71 -4.5 14 1.7
-72 -5 13.5 1.7
-73.5 -5 13 1.7
-74.5 -5.5 12.5 1.7
-76 -6 12 1.7
-77 -6.5 11.5 1.7
-78.5 -6.5 10.5 1.7
-80 -7 10.5 1.7
-81.5 -7 10.5 1.7
-83 -7 10 1.7
-85 -7 9 1.7
-86.5 -7 8 1.7
-88.5 -7 8 1.7
-90.5 -7 8.5 2.2
-92 -7 9.5 1.7
-94 -7 9.5 1.7
-96 -7 9 1.7
-98 -6.5 8 1.7
-100 -6.5 8 1.7
-101.5 -6 8 1.7
-103.5 -6.5 9 1.7
-105 -7 9 1.6
-106.5 -8 9.5 1.6
-108 -8.5 11.5 1.6
-109.5 -9.5 15.5 1.6
-111 -10.5 21 1.6
1 17
-111 -10.5 21 1.6
-110 -11.5 23.5 1.6
-108.5 -12.5 26.5 1.1
-107.5 -13.5 28 1.1
-107 -15 31 1.1
-107.5 -16 35 1.1
-108 -16.5 38.5 1.1
-107.5 -17.5 41.5 1.1
-106 -19 42 1.1
-104.5 -20 43.5 1.1
-103.5 -20.5 44.5 1.1
-103 -20.5 47.5 1.1
-102 -20.5 51.5 1.1
-101.5 -22 54 1.1
-101 -23.5 54.5 0.6
-101 -25 55 0.6
-101 -26 57 0.6
CONNECTIONS:
0 1
1 1
2 1
0 1
1 1
/*----------------------------------------------------------------*/
proc geometry() {
/* NULL geometry procedure: keeps the user from
calling the geometry procedure in isolation. */
printf("\nYou must re-read the entire geometry\n")
printf("file to execute geometry().\n\n")
}