Salamander retinal ganglian cells: morphology influences firing (Sheasby, Fohlmeister 1999)

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Accession:18501
Nerve impulse entrainment and other excitation and passive phenomena are analyzed for a morphologically diverse and exhaustive data set (n=57) of realistic (3-dimensional computer traced) soma-dendritic tree structures of ganglion cells in the tiger salamander (Ambystoma tigrinum) retina.
Reference:
1 . Sheasby BW, Fohlmeister JF (1999) Impulse encoding across the dendritic morphologies of retinal ganglion cells. J Neurophysiol 81:1685-98 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Retina ganglion GLU cell;
Channel(s): I Na,t; I A; I K; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Activity Patterns; Dendritic Action Potentials; Bursting; Coincidence Detection; Simplified Models; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Axonal Action Potentials; Action Potentials; Calcium dynamics;
Implementer(s): Sheasby, Brent W ;
Search NeuronDB for information about:  Retina ganglion GLU cell; I Na,t; I A; I K; I K,Ca; I Calcium;
/
sheasbyfohlmeister1999
SmallSimple
CTT2249A
ctt2249a.asc
ctt2249a.hoc
                            
/*----------------------------------------------------------------
%W%  %G%
ctt2249a.asc  translated Mon Dec 16 17:00:28 1996 by ntscable 2.0
source file syntax: Eutectic
output file syntax: CABLE
soma: diameter = 5.23401 um  length = 17.4566 um  area = 287.041 um2
      10 three-D points; 11 outline points numbered 21-31
      outline diameter = 10.5399 um
4 primary neurites
24 branches totaling 631.245 um in length, 738.807 um2 in area
207 tree points translated to 84 segments (1 requested)
Neurites divided into segments of equal dx between adjacent digitized
branch points.
Segment length constrained to be < 10 um.
No. points    238
No. trees       6
Text  camera lucida of T02249XO, 3/2/89                                                                                       

----------------------------------------------------------------*/
					/* create sections */
create    soma,\
          dend1[13],\
          dend2[1],\
          dend3[17],\
          dend4[13]



/*----------------------------------------------------------------*/
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


					/* neurite geometry*/
    for i = 0,12 {
        dend1[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,0 {
        dend2[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,16 {
        dend3[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,12 {
        dend4[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }



					/* branching topology*/
    for i = 1,12 {
        dend1[fscan()] connect dend1[i] (0), fscan()
    }

    for i = 1,0 {
        dend2[fscan()] connect dend2[i] (0), fscan()
    }

    for i = 1,16 {
        dend3[fscan()] connect dend3[i] (0), fscan()
    }

    for i = 1,12 {
        dend4[fscan()] connect dend4[i] (0), fscan()
    }

}

geometry()


SOMA COORDINATES AND DIAMETERS:

    10
      -8        1      7.5        0
    -5.5  0.39286      7.5   4.7857
    -4.5  0.58333      7.5   5.8333
      -1  0.21875      7.5   7.4375
    -0.5     0.25      7.5      7.5
     1.5  0.13889   7.3889   7.2812
       4  0.35714   6.8929   6.2894
       5  0.28571   6.6786   5.5829
     7.5     0.25      6.5      3.5
     7.5     -1.5      6.5        0


NEURITE COORDINATES AND DIAMETERS:

    1 2
       9     -4.5        0      4.1
       9       -4     -4.5      4.1

    4 13
       9       -4     -4.5      4.1
      10     -7.5       -3      0.3
      11       -9     -2.5      0.3
      13      -12     -3.5      0.3
      13      -15     -3.5      0.3
      12      -18       -4      0.3
    10.5    -19.5       -6      0.3
    10.5      -22     -6.5      0.3
      10      -24     -6.5      0.3
      11      -26       -6      0.3
      11    -28.5     -5.5      0.3
      11    -32.5       -6      0.3
      11    -32.5       -6      0.3

    2 6
       9       -4     -4.5      4.1
      11     -5.5      0.5        2
    13.5     -6.5      1.5      1.8
    15.5       -8        4      1.8
      17     -9.5      4.5      1.7
      18      -11        4      1.7

    1 4
      18      -11        4      1.7
    20.5      -10      4.5      0.3
    22.5     -9.5        5      0.3
    25.5       -9      5.5      0.3

    2 7
    25.5       -9      5.5      0.3
      26       -7      5.5      0.1
      27     -3.5      5.5      0.1
      28       -3        5      0.1
    29.5     -1.5      4.5      0.1
      32        1        5      0.1
      32        1        5      0.1

    4 10
    25.5       -9      5.5      0.3
      27       -9        3      0.3
      30     -7.5      1.5      0.3
      32     -5.5      1.5      0.3
    36.5       -4      0.5      0.3
    41.5     -0.5       -1      0.3
      42      1.5        4      0.1
    44.5        5      3.5      0.1
    44.5      8.5      3.5      0.1
    44.5      8.5      3.5      0.1

    1 2
      18      -11        4      1.7
    18.5    -13.5        5        1

    4 8
    18.5    -13.5        5        1
    16.5    -14.5        5      0.1
      14    -18.5        5      0.1
      12    -21.5        6      0.1
     7.5    -25.5      8.5      0.1
       3    -28.5      7.5      0.1
     0.5    -32.5       10      0.1
    -2.5    -32.5        8      0.1

    1 4
    18.5    -13.5        5        1
      19    -14.5        5      0.8
      20    -18.5        4      0.8
      20    -18.5        4      0.5

    2 6
      20    -18.5        4      0.5
      22      -19      3.5      0.1
      25      -19        4      0.1
      28    -20.5        1      0.1
      31      -22      0.5      0.1
      34    -23.5      0.5      0.1

    2 5
      20    -18.5        4      0.5
      20      -22        5      0.4
      19      -25        6      0.4
    18.5      -28        6      0.4
      17      -30        6      0.4

    3 12
      17      -30        6      0.4
      20      -29      6.5      0.1
      21    -28.5      6.5      0.1
      24    -29.5      6.5      0.1
    26.5    -29.5      6.5      0.1
      30      -31      6.5      0.1
      31    -32.5      6.5      0.1
    31.5      -34        7      0.1
    33.5    -35.5      7.5      0.1
      37      -36        9      0.1
    37.5    -38.5        9      0.1
    37.5    -38.5        9      0.1

    2 6
      17      -30        6      0.4
      14      -30        8      0.1
      13      -33      8.5      0.1
    11.5    -35.5     10.5      0.1
     9.5    -38.5       13      0.1
     7.5      -41       13      0.1

    3 10
       5        2        5      0.7
       6        4      5.5      0.7
     7.5        5        7      0.7
       8        7        7      0.4
     8.5      9.5      6.5      0.4
    11.5     11.5      6.5      0.4
    12.5     13.5        8      0.1
    14.5       14        7      0.1
    16.5       15      5.5      0.1
      19       17        3      0.1

    1 3
      -5      2.5     -3.5      1.3
      -6      4.5        4      1.3
      -6      4.5        4      1.3

    3 9
      -6      4.5        4      1.3
      -5        7      6.5      0.7
      -5     10.5      7.5      0.7
    -6.5       12      5.5      0.6
      -7       14      6.5      0.6
    -6.5       15        8      0.4
    -6.5       18        8      0.4
    -6.5     20.5      7.5      0.4
      -7       22      9.5      0.4

    2 5
      -7       22      9.5      0.4
      -5       25       10      0.1
    -3.5       28      9.5      0.1
    -2.5       31     12.5      0.1
    -1.5     32.5     13.5      0.1

    2 7
      -7       22      9.5      0.4
      -9       23      9.5      0.1
     -10     25.5      8.5      0.1
     -12       29        9      0.1
     -15     29.5        9      0.1
   -15.5     32.5        9      0.1
     -17       35        9      0.1

    1 3
      -6      4.5        4      1.3
    -9.5      3.5        4      1.1
     -12      4.5        4      1.1

    1 3
     -12      4.5        4      1.1
   -15.5      4.5      7.5      0.8
     -17      4.5      7.5      0.8

    2 7
     -17      4.5      7.5      0.8
   -17.5      5.5        9      0.3
     -20      7.5        9      0.3
   -21.5        9      9.5      0.3
   -23.5     10.5      9.5      0.3
   -26.5       11      9.5      0.3
   -26.5       11      9.5      0.3

    2 6
   -26.5       11      9.5      0.3
     -29       11      5.5      0.1
   -30.5       12        6      0.1
     -33     13.5        5      0.1
   -34.5       16        7      0.1
   -35.5     17.5        7      0.1

    2 4
   -26.5       11      9.5      0.3
   -28.5     13.5      6.5      0.1
   -27.5       18      6.5      0.1
   -28.5     20.5      6.5      0.1

    5 11
     -17      4.5      7.5      0.8
     -19        2       10      0.1
   -21.5       -1        8      0.1
     -23     -3.5      8.5      0.1
   -21.5     -9.5      8.5      0.1
   -21.5    -13.5      9.5      0.1
   -22.5      -20       10      0.1
     -23    -25.5      7.5      0.1
     -27    -27.5        8      0.1
     -29    -29.5      8.5      0.1
     -29    -29.5        8      0.1

    1 4
     -12      4.5        4      1.1
   -13.5      7.5        6      0.1
   -12.5      9.5      6.5      0.1
   -12.5       12      8.5      0.1

    1 3
   -12.5       12      8.5      0.1
     -11     13.5        8      0.1
   -10.5     15.5        8      0.1

    1 3
   -12.5       12      8.5      0.1
     -14     13.5       10      0.1
   -15.5     17.5        8      0.1

    1 4
   -15.5     17.5        8      0.1
   -15.5       19       10      0.1
   -15.5     22.5        8      0.1
     -16     25.5        8      0.1

    1 3
   -15.5     17.5        8      0.1
     -20     17.5      8.5      0.1
     -20     17.5      8.5      0.1

    1 3
     -20     17.5      8.5      0.1
   -22.5       16        9      0.1
   -24.5       16        9      0.1

    2 4
     -20     17.5      8.5      0.1
     -23     20.5        7      0.1
     -27       24      6.5      0.1
     -27       25        7      0.1

    2 3
    -3.5       -4     -2.5      0.9
    -3.5       -5        6      0.9
      -5     -6.5        7      0.9

    1 5
      -5     -6.5        7      0.9
      -4       -9      7.5      0.5
      -5      -12      7.5      0.5
      -6    -13.5        7      0.5
      -6    -13.5        7      0.5

    2 4
      -6    -13.5        7      0.5
    -7.5      -14        7      0.1
     -15      -14        6      0.1
     -16    -12.5        7      0.1

    1 5
      -6    -13.5        7      0.5
    -5.5      -15        7      0.4
    -4.5    -16.5        7      0.4
      -4      -20        7      0.4
      -4      -21        7      0.1

    1 4
      -4      -21        7      0.1
    -2.5      -24      6.5      0.1
      -1    -28.5        6      0.1
      -1      -29        6      0.1

    2 9
      -4      -21        7      0.1
    -5.5      -22        8      0.3
      -7      -24        8      0.3
    -9.5      -26      8.5      0.3
   -10.5      -28      7.5      0.3
   -11.5      -30      8.5      0.3
   -12.5      -32      8.5      0.3
   -14.5      -34      9.5      0.3
   -15.5    -34.5      9.5      0.3

    1 3
   -15.5    -34.5      9.5      0.3
   -19.5    -34.5      9.5      0.1
     -22    -34.5      9.5      0.1

    1 5
   -15.5    -34.5      9.5      0.3
   -15.5      -37       10      0.1
   -15.5    -39.5      9.5      0.1
   -14.5      -42       10      0.1
   -14.5      -42       10      0.1

    1 4
      -5     -6.5        7      0.9
      -7       -7        6      0.6
    -9.5     -7.5      7.5      0.6
     -13       -7        8        1

    1 3
     -13       -7        8        1
     -16       -5        6      0.1
     -19     -3.5        6      0.1

    1 2
     -13       -7        8        1
   -18.5     -8.5      6.5        1

    5 13
   -18.5     -8.5      6.5        1
   -19.5     -6.5        7      0.6
     -23       -4        7      0.2
     -25     -0.5        8      0.2
     -28      0.5      8.5      0.1
   -31.5        3      9.5      0.1
   -35.5        6      9.5      0.1
   -40.5      6.5      6.5      0.1
   -42.5      9.5      6.5      0.1
     -45     12.5      6.5      0.1
     -49     14.5      6.5      0.1
   -53.5       14        7      0.1
     -56     13.5      6.5      0.1

    3 10
   -18.5     -8.5      6.5        1
   -20.5      -11      6.5      0.1
     -22    -12.5      6.5      0.1
     -24      -15      8.5      0.1
     -27      -16     10.5      0.1
     -29    -16.5     11.5      0.1
     -32      -18     11.5      0.1
   -36.5    -17.5       12      0.1
     -38      -16     12.5      0.1
     -39      -16        9      0.1


CONNECTIONS:
        0    1
        0    1
        2    1
        3    1
        3    1
        2    1
        6    1
        6    1
        8    1
        8    1
       10    1
       10    1


        0    1
        1    1
        1    1
        0    1
        4    1
        5    1
        6    1
        6    1
        5    1
        4    1
       10    1
       10    1
       12    1
       12    1
       14    1
       14    1

        0    1
        1    1
        1    1
        3    1
        3    1
        5    1
        5    1
        0    1
        8    1
        8    1
       10    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")
}


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