/*---------------------------------------------------------------- $Header$ hugtcc.asc translated Thu Jan 21 10:12:05 1993 by ntscable 2.0 source file syntax: Eutectic output file syntax: NEURON soma: diameter = 21.7456 um length = 42.6901 um area = 2916.41 um2 13 three-D points; 14 outline points numbered 347-360 outline diameter = 24.4073 um 11 primary neurites 108 branches totaling 7094.47 um in length, 33581 um2 in area 1224 tree points translated to 206 segments (1 requested) Neurites divided into segments of equal dx between adjacent digitized branch points. Segment length constrained to be < 7094.47 um. No. points 1238 No. trees 12 Rat VB neuron (thalamocortical cell), given by J. Huguenard, stained with biocytin and traced by A. Destexhe, December 1992. The neuron is described in: J.R. Huguenard & D.A. Prince, 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. A Destexhe, 07 Mar 96, neuron structure edited: changed 3d points of dendrites and soma to make them stick appropriately (with no change in electrotonic structure). dend1 moved, soma moved to stick to dend1, dendrites 6,8,9,4,11 moved in that order (nonoverlapping). The diameters at the tip of dendrites was erroneous due to the presence of membrane artifacts (biocytin bubbles). They were rescaled down to match morphological data of other cells. => New membrane area: - 24527.179 um2 including 3171.4274 um2 for the soma (area procedure) - 23980.547 um2 including 2624.7773 um2 for the soma (PI*diam*L) The morphology, passive cable properties and modeling of this neuron are described in: Destexhe A, Neubig M, Ulrich D and Huguenard JR. Dendritic low-threshold calcium currents in thalamic relay cells. Journal of Neuroscience 18: 3574-3588, 1998. http://cns.fmed.ulaval.ca This geometry can be used by anyone interested, under the only condition that the two above papers are cited. Please also send us a copy of publications that use that cell as courtesy. Alain Destexhe, Laval University, 1997 ----------------------------------------------------------------*/ /* make geometry explicit */ primary_branches_cell = 11 branches_cell = 108 max_dx_cell = 7094.47 points_cell = 1224 nseg_cell = 206 double sections_cell[11] sections_cell[0] = 1 sections_cell[1] = 3 sections_cell[2] = 13 sections_cell[3] = 21 sections_cell[4] = 1 sections_cell[5] = 31 sections_cell[6] = 9 sections_cell[7] = 33 sections_cell[8] = 47 sections_cell[9] = 27 sections_cell[10] = 19 nsec_cell = 206 strdef name_soma, name_section name_soma = "soma" name_section = "dend" use_axon = 0 /* create sections */ create soma,\ dend1[1],\ dend2[3],\ dend3[13],\ dend4[21],\ dend5[1],\ dend6[31],\ dend7[9],\ dend8[33],\ dend9[47],\ dend10[27],\ dend11[19] /*----------------------------------------------------------------*/ proc geometry() { local i, j /* soma geometry */ soma { nseg = 1 pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } /* connect primary neurites */ soma connect dend1[0] (0), 0.5 soma connect dend2[0] (0), 0.5 soma connect dend3[0] (0), 0.5 soma connect dend4[0] (0), 0.5 soma connect dend5[0] (0), 0.5 soma connect dend6[0] (0), 0.5 soma connect dend7[0] (0), 0.5 soma connect dend8[0] (0), 0.5 soma connect dend9[0] (0), 0.5 soma connect dend10[0] (0), 0.5 soma connect dend11[0] (0), 0.5 /* neurite geometry*/ for i = 0,0 { dend1[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,2 { dend2[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,12 { dend3[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,20 { dend4[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,0 { dend5[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,30 { dend6[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,8 { dend7[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,32 { dend8[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,46 { dend9[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,26 { dend10[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } for i = 0,18 { dend11[i] { nseg = fscan() pt3dclear() for j = 1, fscan() { pt3dadd(fscan(),fscan(),fscan(),fscan()) } } } /* branching topology*/ for i = 1,0 { dend1[fscan()] connect dend1[i] (0), fscan() } for i = 1,2 { dend2[fscan()] connect dend2[i] (0), fscan() } for i = 1,12 { dend3[fscan()] connect dend3[i] (0), fscan() } for i = 1,20 { dend4[fscan()] connect dend4[i] (0), fscan() } for i = 1,0 { dend5[fscan()] connect dend5[i] (0), fscan() } for i = 1,30 { dend6[fscan()] connect dend6[i] (0), fscan() } for i = 1,8 { dend7[fscan()] connect dend7[i] (0), fscan() } for i = 1,32 { dend8[fscan()] connect dend8[i] (0), fscan() } for i = 1,46 { dend9[fscan()] connect dend9[i] (0), fscan() } for i = 1,26 { dend10[fscan()] connect dend10[i] (0), fscan() } for i = 1,18 { dend11[fscan()] connect dend11[i] (0), fscan() } } geometry() SOMA COORDINATES AND DIAMETERS: 13 -23.25 -7.35 -34.2 0 -21.9 -6.18 -31.05 14.959 -21 -5.8875 -30.4875 21.439 -20.1 -5.03862 -28.6974 24.974 -16.95 -4.48638 -27.5526 25.363 -16.05 -4.26426 -26.5824 26.719 -13.8 -3.05889 -24.0111 28.865 -9.75 -1.51125 -21.6675 28.311 -4.8 1.0875 -17.5662 25.297 -3.45 0.795 -15.435 23.776 -0.75 1.875 -11.4192 15.383 0.15 1.56 -10.53 10.826 1.5 3 -9 0 NEURITE COORDINATES AND DIAMETERS: 1 17 1.5 3 -9 0.91 1.5 5.5 0 0.91 3.5 8.5 5.5 0.91 6 10 9 0.91 9 9.5 13 0.91 12.5 9 17 0.91 15 9.5 22 0.91 17 11.5 25 0.91 18.5 13.5 29 0.91 21.5 14.5 35.5 0.91 24 16 41.5 0.91 26.5 16 49.5 0.91 29.5 17 55 0.91 33 18 58.5 0.91 37.5 18.5 61.5 0.91 42 18.5 63.5 0.91 47 18.5 66.5 0.91 1 12 0 13.5 -5 0.91 2 14 -2.5 0.91 4.5 14.5 0.5 0.91 6.5 16 4 0.91 8.5 17 7.5 0.91 10 18.5 11 0.91 12 18.5 12.5 0.91 14 19 15 0.91 16 19 16.5 0.91 18 20 18.5 0.91 21 21 21 0.91 24.5 22.5 26.5 0.91 1 15 24.5 22.5 26.5 0.93 28 24 31.5 0.93 31 26 34.5 0.93 33.5 29 36 0.93 35.5 32 36.5 0.93 38 34.5 39.5 0.93 41.5 34.5 42 0.93 45 33.5 48.5 0.93 48 33.5 52.5 0.93 50 34.5 56.5 0.93 52.5 35.5 58 0.93 55.5 34.5 59.5 0.93 58.5 34.5 61.5 0.93 60 35 64 0.93 59.5 36.5 68 0.93 1 14 24.5 22.5 26.5 0.86 24.5 25 34 0.86 25.5 28 42 0.86 26.5 30.5 47 0.86 28.5 33 50.5 0.86 31 35 51 0.86 33.5 37.5 52 0.86 36 41.5 54.5 0.86 38 45.5 57 0.86 39.5 49.5 59 0.86 41 52.5 60 0.86 42 55.5 63 0.86 42.5 58.5 63 0.86 42.5 62.5 61 0.86 1 4 7 -3 -5 2.8 7.5 -4 2.5 2.8 9 -6 7.5 2.8 11 -8 10.5 2.8 1 6 11 -8 10.5 1.3 14 -8 11 1.3 17 -7.5 12.5 1.3 20.5 -6.5 14 1.3 23.5 -4.5 13.5 1.3 27 -2.5 13 1.3 1 2 27 -2.5 13 2.2 27.1 -2.5 13 2.2 1 10 27.1 -2.5 13 0.96 29.5 -4 15 0.96 33 -5.5 18 0.96 36.5 -8 21.5 0.96 40 -9.5 23 0.96 43 -9.5 24 0.96 46.5 -7.5 24 0.96 49.5 -6 24 0.96 53 -4.5 24 0.96 56.5 -4 25 0.96 1 19 27.1 -2.5 13 0.93 28 0 14.5 0.93 29.5 2 15.5 0.93 31.5 4.5 15.5 0.93 33.5 7 19 0.93 35 9.5 23 0.93 37 11 29.5 0.93 39 12.5 33.5 0.93 41.5 13.5 39 0.93 44.5 15 45 0.93 47 15.5 51.5 0.93 50 16.5 55 0.93 53 18 56 0.93 55.5 19 56 0.93 57.5 20.5 56 0.93 59 22 56 0.93 60.5 22 57 0.93 63.5 21 60.5 0.93 67 20 66.5 0.93 1 16 27 -2.5 13 0.94 29 -0.5 11 0.94 31.5 1 10.5 0.94 34 4 10.5 0.94 37 6.5 12 0.94 39.5 8.5 15.5 0.94 42.5 10 18.5 0.94 45 11 21.5 0.94 47.5 11.5 23.5 0.94 50 11.5 27 0.94 53 12.5 30.5 0.94 57 14 33 0.94 61 15.5 35 0.94 65.5 17 38.5 0.94 69 17.5 42 0.94 72 17.5 45 0.94 1 8 72 17.5 45 0.8 75.5 17 47 0.8 79.5 17 49 0.8 83 16.5 50.5 0.8 87 16.5 50.5 0.8 91.5 16 50.5 0.8 96 17 53.5 0.8 100 19 60 0.8 1 5 72 17.5 45 0.8 74.5 18.5 38 0.8 77 20 34.5 0.8 81 21.5 34.5 0.8 86.5 24.5 34.5 0.8 1 7 11 -8 10.5 1.2 12 -10 10.5 1.2 15 -11 14 1.2 17.5 -12 19.5 1.2 18.5 -14 23.5 1.2 18 -16.5 26.5 1.2 17 -19 30.5 1.2 1 6 17 -19 30.5 0.93 14 -20 31.5 0.93 12 -22 35 0.93 11.5 -24.5 40.5 0.93 12.5 -27.5 42.5 0.93 15 -29.5 41 0.93 1 8 17 -19 30.5 0.92 18 -21 28 0.92 19.5 -23.5 26.5 0.92 21 -24.5 23.5 0.92 23 -24 22 0.92 25.5 -22.5 22 0.92 27.5 -21.5 27 0.92 30 -21.5 34.5 0.92 1 9 30 -21.5 34.5 0.91 31.5 -20 39.5 0.91 33 -19.5 45 0.91 34.5 -20 50.5 0.91 35 -19 58 0.91 36.5 -18 63 0.91 37.5 -15 66.5 0.91 40 -13 68 0.91 42.5 -10.5 72 0.91 1 3 30 -21.5 34.5 0.91 32.5 -22 36 0.91 35 -23 37 0.91 1 3 0.15 1.56 -10.53 4.3 3.15 -1.44 -0.0300007 4.3 7.15 -4.94 7.97 4.3 1 4 7.15 -4.94 7.97 1.7 4.65 -7.44 11.47 1.7 3.15 -9.94 13.97 1.7 3.15 -13.44 15.97 1.7 1 19 3.15 -13.44 15.97 1.2 4.15 -16.44 18.47 1.2 4.15 -19.94 21.97 1.2 3.15 -23.94 24.97 1.2 2.15 -27.94 27.47 1.2 1.65 -32.44 27.97 1.2 2.15 -36.94 27.97 1.2 2.15 -40.94 30.97 1.2 2.15 -43.94 33.97 1.2 3.15 -46.44 36.47 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30.06 39.97 1.2 -21.85 33.56 32.47 1.2 -23.35 36.06 29.47 1.2 -26.35 39.06 31.47 1.2 -28.35 43.06 35.97 1.2 -32.35 46.06 39.97 1.2 -35.85 48.56 45.47 1.2 -40.35 50.06 49.97 1.2 -45.35 51.56 52.47 1.2 -52.35 53.06 54.47 1.2 1 4 7.15 -4.94 7.97 2.3 10.15 -6.94 12.97 2.3 13.15 -9.44 16.47 2.3 16.15 -11.44 18.47 2.3 1 2 16.15 -11.44 18.47 1.9 16.25 -11.44 18.47 1.9 1 13 16.25 -11.44 18.47 0.8 19.15 -13.44 16.47 0.8 22.65 -14.94 15.97 0.8 25.65 -16.44 15.97 0.8 28.15 -17.94 15.97 0.8 31.15 -20.44 16.47 0.8 33.65 -22.94 16.97 0.8 37.15 -25.94 16.47 0.8 40.65 -27.94 14.47 0.8 44.65 -29.44 13.47 0.8 48.65 -31.94 13.47 0.8 52.15 -35.44 13.97 0.8 55.15 -40.44 15.97 0.8 1 3 16.25 -11.44 18.47 1.7 18.65 -9.94 18.47 1.7 22.15 -8.94 18.47 1.7 1 2 22.15 -8.94 18.47 1.7 22.25 -8.94 18.47 1.7 1 10 22.25 -8.94 18.47 0.8 24.15 -6.44 24.47 0.8 26.65 -4.94 29.47 0.8 29.65 -3.44 31.47 0.8 33.65 -2.44 33.47 0.8 37.65 -0.44 34.47 0.8 41.65 1.06 37.47 0.8 45.15 2.56 41.47 0.8 50.15 2.56 44.97 0.8 56.15 1.06 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65 0.96 -5 -5 65 0.96 -7.5 -4.5 65 0.96 -9.5 -3 63 0.96 -10 0 56.5 0.96 -9 2.5 50 0.96 -7 4.5 45 0.96 -5 5.5 42 0.96 -4.5 7 39 0.96 -6.5 7.5 36 0.96 -9 8.5 36 0.96 -10 10 36 0.96 -9.5 12 36 0.96 -8 13 36 0.96 -6 13.5 40 0.96 -4.5 14 44.5 0.96 -4.5 15 48 0.96 -5 16 47 0.96 -7 17 46 0.96 -7.5 18 47.5 0.96 -7.5 19 49.5 0.96 -7 20.5 53.5 0.96 -6.5 22 55 0.96 -6.5 23.5 57.5 0.96 -6.5 25 59.5 0.96 -7 27 67.5 0.96 -9 27.5 71 0.96 -10 29.5 75.5 0.96 -10 32 77 0.96 1 3 -23.25 -7.35 -34.2 4.4 -25.25 -7.35 -34.2 4.4 -26.75 -7.35 -34.2 4.4 1 4 -26.75 -7.35 -34.2 3.6 -38.75 -8.85 -30.7 3.6 -47.25 -9.35 -26.7 3.6 -51.75 -8.85 -22.2 3.6 1 2 -51.75 -8.85 -22.2 3.8 -51.85 -8.85 -22.2 3.8 1 4 -51.85 -8.85 -22.2 2.3 -58.75 -14.35 -22.2 2.3 -63.75 -18.35 -22.2 2.3 -66.25 -20.35 -22.2 2.3 1 10 -66.25 -20.35 -22.2 0.8 -70.25 -26.85 -18.2 0.8 -74.25 -31.85 -16.2 0.8 -77.75 -37.35 -15.7 0.8 -79.25 -41.85 -14.2 0.8 -80.75 -47.35 -12.7 0.8 -84.25 -51.35 -11.7 0.8 -92.25 -56.35 -11.7 0.8 -104.25 -62.35 -11.7 0.8 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10 1 1 1 13 1 14 1 14 1 16 1 16 1 13 1 0 1 20 1 21 1 22 1 22 1 21 1 25 1 25 1 27 1 27 1 20 1 0 1 1 1 1 1 0 1 4 1 5 1 5 1 4 1 0 1 1 1 2 1 3 1 4 1 4 1 3 1 7 1 7 1 2 1 1 1 11 1 11 1 0 1 14 1 15 1 16 1 17 1 17 1 16 1 15 1 21 1 21 1 14 1 24 1 25 1 25 1 27 1 27 1 24 1 30 1 30 1 0 1 1 1 2 1 3 1 4 1 5 1 5 1 7 1 8 1 8 1 7 1 11 1 12 1 12 1 11 1 4 1 3 1 2 1 18 1 18 1 1 1 0 1 22 1 23 1 23 1 22 1 26 1 27 1 28 1 29 1 30 1 30 1 29 1 28 1 27 1 35 1 36 1 36 1 35 1 39 1 40 1 40 1 39 1 26 1 44 1 44 1 0 1 0 1 2 1 3 1 3 1 2 1 6 1 7 1 8 1 8 1 7 1 11 1 12 1 12 1 11 1 6 1 16 1 17 1 18 1 18 1 17 1 16 1 22 1 22 1 24 1 24 1 0 1 1 1 2 1 3 1 3 1 2 1 6 1 6 1 1 1 0 1 10 1 11 1 12 1 13 1 13 1 12 1 11 1 10 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") }