how to model 2 clones neuron from .asc file

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bellarude
Posts: 1
Joined: Fri Sep 14, 2018 4:17 am

how to model 2 clones neuron from .asc file

Post by bellarude » Sun Sep 16, 2018 7:51 pm

Good morning everyone, I'm facing a very simple problem but my less experience with NEURON leads me here, hoping to find tips and helps.

I'm running on Windows a NEURON version 7.6.
I have an .asc file with the geometric properties of one ganglion neuron and a .hoc file which set his chemical properties.

What i would do is simply generate a clone of this first one at one specific spatial coordinate, having at the end 2 neurons one close to each other, and afterward investigate neurons spike under external electrical field.

What I've done was generate a template in the .asc file, importing it in the .hox file and then put it in a foor loop (just 2 iteration) which assign chemical properties to each neuron. I don't think this is the smartest way to do that, first of all because it gives me an error and second because i don't understand why i cannot directly generate a template using bot files (.asc and .hoc). I tried to be honest, but i didn't get how this 2 files are thought to communicate. Also in my code i still didn't specific any coordinates because I would just check to get 2 neurons at the default position given by NEURON.

The error which appears is:

Code: Select all

C:\nrn\bin\nrniv.exe: Segmentation violation
 in C:/Users/Rudy/Downloads/sheasbyfohlmeister1999a_r1/sheasbyfohlmeister1999/SmallComplex/CTS7259Gsingle - Copy/cts7259g.hoc near line 9
 }
I would ask your help not only for solve the problem but also for improve my knowledge in NEURON programming, as I said I'm a really beginner. Thanks to everyone might help me.

I report the 2 file here, give me all the advices you recommend to improve my coding. Many thanks.

.asc file

Code: Select all

begintemplate CELL
public soma,dend1,dend2,dend3,dend4,dend5,dend6,initseg, narrow,axon
					/* create sections */
create    soma,\
          dend1[3],\
          dend2[1],\
          dend3[13],\
          dend4[5],\
          dend5[21],\
          dend6[9]
create initseg, narrow, axon


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


					/* neurite geometry*/
    for i = 0,2 {
        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 = 0,12 {
        dend3[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,4 {
        dend4[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,20 {
        dend5[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,8 {
        dend6[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }



					/* branching topology*/
    for i = 1,2 {
        dend1[fscan()] connect dend1[i] (0), fscan()
    }

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

    for i = 1,12 {
        dend3[fscan()] connect dend3[i] (0), fscan()
    }

    for i = 1,4 {
        dend4[fscan()] connect dend4[i] (0), fscan()
    }

    for i = 1,20 {
        dend5[fscan()] connect dend5[i] (0), fscan()
    }

    for i = 1,8 {
        dend6[fscan()] connect dend6[i] (0), fscan()
    }

}

geometry()
endtemplate CELL

SOMA COORDINATES AND DIAMETERS:

    17
    -6.5     -0.5      1.5        0
      -6  -1.4167    1.375   3.1765
    -5.5  -2.5833     1.25   6.8516
    -4.5  -2.6667     0.75   9.6796
    -3.5  -2.2143  0.71429   11.518
    -1.5  -1.1429  0.39286   15.748
      -1     -1.1      0.5   16.298
       1    -1.25      0.5   18.927
       2  0.66667     0.25   20.175
     2.5        1  0.17857   19.559
       3      2.5 -0.39286   16.442
     4.5      3.5 -0.60714   14.621
     5.5   4.1667    -0.75   13.442
       6     3.75    -0.75   11.424
     6.5    3.625       -1   8.7214
       7    3.375     -0.5   5.1539
     7.5        4        0        0


NEURITE COORDINATES AND DIAMETERS:

    1 3
    -3.5     -8.5      0.5      1.7
    -6.5      -10      0.5      1.6
    -9.5      -10        1      1.6

    1 2
    -9.5      -10        1      1.6
     -10    -12.5      3.5      0.1

    2 10
    -9.5      -10        1      1.6
   -10.5     -9.5      1.5        1
   -11.5       -7        1      0.9
     -14       -6        0      0.7
   -14.5     -5.5        0      0.3
     -17       -5        0      0.3
     -18     -7.5        1      0.1
   -19.5     -8.5        2      0.1
     -22       -8      0.5      0.1
     -23       -7        1      0.1

    5 16
       1       -3      0.5        1
    -1.5       -4        5        1
    -2.5       -5        8        1
    -2.5     -6.5       10      0.7
      -1     -8.5       10      0.7
       1    -10.5      8.5      0.4
     3.5      -10        9      0.4
       5    -10.5        9      0.3
     6.5      -13       10      0.3
       8    -14.5       11      0.3
     9.5    -13.5     11.5      0.1
      10    -12.5       12      0.1
    11.5    -15.5     11.5      0.1
    14.5    -17.5       12      0.1
      17      -19     10.5      0.1
    18.5      -19       11      0.1

    3 7
       1     -6.5        0      2.5
       0      -11      2.5      1.4
       0      -14      3.5      0.9
    -0.5      -16        5      0.9
      -2      -17      7.5      0.9
    -3.5      -21      8.5      0.9
    -3.5      -22       10      0.9

    2 5
    -3.5      -22       10      0.9
    -2.5      -24       10      0.1
       0      -24      9.5      0.1
       1    -26.5      9.5      0.1
     1.5      -29      9.5      0.1

    2 6
    -3.5      -22       10      0.9
      -5    -23.5       10      0.9
    -5.5      -25       10      0.9
    -5.5      -26       10      0.6
    -6.5    -26.5       10      0.6
      -8      -30       12      0.6

    9 25
      -8      -30       12      0.6
   -10.5      -31     11.5      0.1
     -12    -33.5     12.5      0.1
     -14    -35.5       12      0.1
     -18      -39     12.5      0.1
     -20      -40     13.5      0.1
   -21.5      -44     13.5      0.1
   -23.5    -49.5     13.5      0.1
   -26.5      -56       15      0.1
     -29      -60       16      0.1
     -30    -62.5     15.5      0.1
   -30.5      -64     15.5      0.1
   -31.5      -65     15.5      0.1
   -31.5    -69.5     15.5      0.1
   -33.5      -72     15.5      0.1
   -36.5    -74.5     15.5      0.1
   -37.5    -78.5     15.5      0.1
     -39      -82     14.5      0.1
     -40    -84.5     14.5      0.1
   -41.5    -86.5     14.5      0.1
     -44    -89.5       15      0.1
   -46.5      -92     16.5      0.1
     -49    -95.5     16.5      0.1
   -52.5    -99.5     17.5      0.1
   -53.5     -101     17.5      0.1

    1 4
      -8      -30       12      0.6
    -7.5    -31.5       13      0.1
      -9      -36       14      0.1
      -9      -36       14      0.1

    2 6
      -9      -36       14      0.1
     -12    -37.5       14      0.1
     -14    -41.5       15      0.1
     -17    -45.5       15      0.1
     -19    -48.5       15      0.1
     -19    -48.5       15      0.1

    1 3
     -19    -48.5       15      0.1
     -22    -50.5       15      0.1
     -25      -54       15      0.1

    1 4
     -19    -48.5       15      0.1
   -19.5      -52       15      0.1
     -21      -55       15      0.1
     -21      -55       15      0.1

    2 6
     -21      -55       15      0.1
     -22    -57.5       15      0.1
     -24      -60       15      0.1
   -26.5    -64.5     15.5      0.1
   -27.5    -67.5     15.5      0.1
     -28    -68.5     15.5      0.1

    2 5
     -21      -55       15      0.1
     -22    -58.5       15      0.1
     -23    -62.5       15      0.1
   -23.5      -65       15      0.1
     -24    -66.5       15      0.1

    2 4
      -9      -36       14      0.1
   -11.5      -40       15      0.1
   -13.5      -44       15      0.1
   -14.5      -45       15      0.1

    2 6
   -14.5      -45       15      0.1
     -16      -47       15      0.1
   -17.5    -50.5       15      0.1
     -20      -54     15.5      0.1
   -20.5    -56.5     15.5      0.1
   -21.5    -59.5     15.5      0.1

    2 5
   -14.5      -45       15      0.1
     -12    -48.5     14.5      0.1
   -11.5    -50.5     14.5      0.1
   -10.5    -53.5     14.5      0.1
     -10      -56       15      0.1

    2 7
    -5.5      1.5      0.5      1.4
    -6.5        1        3        2
      -8     -1.5        6      1.3
      -9      0.5        7        1
     -11      0.5        7        1
   -12.5       -1        7        1
     -14       -2        7        1

    3 10
     -14       -2        7        1
     -15     -4.5        7      0.6
   -15.5     -6.5        7      0.6
     -14       -7        6      0.6
     -13       -9        6      0.6
   -11.5    -11.5        7      0.6
   -10.5      -14      7.5      0.6
     -10      -16        7      0.6
     -10      -19        9      0.1
   -10.5      -19        9      0.1

    2 4
     -14       -2        7        1
     -16     -1.5       10      0.8
     -18      0.5        9      0.6
   -20.5       -1     11.5      0.6

    1 5
   -20.5       -1     11.5      0.6
     -21      0.5     10.5      0.1
     -22      2.5     11.5      0.1
     -24      4.5       10      0.1
     -24      4.5       10      0.1

    3 8
   -20.5       -1     11.5      0.6
   -20.5     -3.5       11      0.3
   -21.5     -6.5       13      0.3
     -22    -10.5       13      0.3
   -23.5    -14.5       13      0.3
     -25      -21     14.5      0.3
   -26.5    -24.5     14.5      0.2
     -28      -28     14.5      0.1

    2 9
       3     11.5        0      1.2
       2     13.5     -1.5      1.2
       2     15.5     -1.5      1.2
       4       16     -1.5      1.2
     6.5     17.5      0.5      1.2
       5       20      1.5      1.2
     5.5       24      1.5      1.2
     6.5     25.5      1.5      1.2
     6.5     25.5      1.5      1.2

    5 15
     6.5     25.5      1.5      1.2
     4.5     26.5      3.5      0.4
       3     27.5      6.5      0.4
       2       30      8.5      0.4
       2       32      8.5      0.2
     1.5     34.5      9.5      0.2
     1.5     37.5     10.5      0.2
       1     40.5      9.5      0.2
       1       43        8      0.2
       2       46        8      0.2
     3.5     49.5        8      0.2
     5.5       52      8.5      0.2
       6     55.5      8.5      0.2
       6       60        7      0.2
       5     62.5      7.5      0.1

    1 3
     6.5     25.5      1.5      1.2
       8       27        2      1.1
       9       28        2      2.4

    2 4
       9       28        2      2.4
    11.5     30.5        4      0.9
      13     33.5      4.5      0.9
      14       37      4.5      0.9

    1 5
      14       37      4.5      0.9
    16.5     37.5      4.5      0.9
    18.5     36.5      4.5      0.9
    19.5       36      4.5      0.9
      21     37.5      4.5      0.9

    3 8
      21     37.5      4.5      0.9
      21     39.5      2.5      0.1
      23     42.5      3.5      0.1
      24     45.5      3.5      0.1
    24.5       48        4      0.1
      26       52        4      0.1
    24.5       56        4      0.1
    24.5       59        4      0.1

    1 5
      21     37.5      4.5      0.9
    21.5     35.5        4      0.5
    24.5       36      4.5      0.5
      25     32.5        5      0.8
    25.5       32        5      0.8

    3 9
    25.5       32        5      0.8
      25       29        5      0.1
      26       24        5      0.1
    27.5       22        8      0.1
    29.5       22        9      0.1
      31     24.5        9      0.1
    32.5     24.5        9      0.1
      35       27        9      0.1
    36.5       27        9      0.1

    6 19
    25.5       32        5      0.8
      27     33.5        4      0.5
    29.5       36        4      0.5
    32.5     40.5      4.5      0.5
    32.5     42.5        4      0.5
      35       46        3      0.5
      36     48.5      2.5      0.5
    37.5       52      2.5      0.5
    38.5     55.5      2.5      0.5
    39.5       59      2.5      0.5
    40.5       63      2.5      0.5
      42       66      2.5      0.5
    42.5       67      2.5      0.5
    42.5     68.5      2.5      0.3
    43.5     71.5      2.5      0.3
      43     72.5      2.5      0.3
      44       74        3      0.3
    44.5       76      3.5      0.3
      46       81        3      0.3

    4 8
      46       81        3      0.3
    46.5     82.5        3      0.1
      48       86      2.5      0.1
    49.5     89.5        5      0.1
      51       93      3.5      0.1
    54.5       97        4      0.1
    56.5    101.5      4.5      0.1
    58.5      108        5      0.1

    6 13
      46       81        3      0.3
    44.5       86        4      0.2
    44.5     89.5        4      0.2
      42       91        4      0.2
    43.5     95.5      2.5      0.2
    43.5      101      4.5      0.2
      44      105        2      0.2
    44.5    109.5        4      0.1
    45.5      115        3      0.1
    47.5    119.5        2      0.1
    48.5      126      2.5      0.1
    48.5      131        2      0.1
      47    134.5        2      0.1

    7 22
      14       37      4.5      0.9
    13.5     39.5        4      0.3
    14.5       43        5      0.3
      16     44.5      5.5      0.2
      17       48        4      0.1
    17.5       50        4      0.1
      20       54      4.5      0.1
      24       58      3.5      0.1
      27     60.5      5.5      0.1
    30.5     62.5      5.5      0.1
    31.5     63.5      5.5      0.1
    34.5     66.5      5.5      0.1
    35.5     67.5      5.5      0.1
      37       68      5.5      0.1
      40       72        4      0.1
    41.5     75.5        4      0.1
      43     77.5        4      0.1
    45.5       79        4      0.1
      49     78.5        4      0.1
    50.5       79        4      0.1
      52       75      3.5      0.1
    54.5     73.5        5      0.1

    3 10
       9       28        2      2.4
     8.5     30.5      1.5      0.5
     8.5       33      2.5      0.5
     8.5     35.5        3      0.5
     9.5       37        3      0.5
       8     38.5        3      0.5
       8       40        3      0.5
       7     41.5        3      0.5
       7       45        3      0.5
     6.5     46.5        4      0.1

    3 12
     6.5     46.5        4      0.1
       3     47.5        4      0.1
       1       48        4      0.1
      -1     48.5      5.5      0.1
      -3     47.5      5.5      0.1
      -4     49.5        6      0.1
      -6     49.5      5.5      0.1
      -6     47.5      5.5      0.1
      -8       50      5.5      0.1
    -9.5       47      5.5      0.1
   -11.5       49        6      0.1
     -15     48.5      6.5      0.1

    2 6
     6.5     46.5        4      0.1
       8     49.5      3.5      0.3
       9     51.5      3.5      0.3
       9     55.5      5.5      0.3
     6.5     56.5      4.5      0.3
       4       58        6      0.3

    1 6
       4       58        6      0.3
     3.5     56.5        6      0.1
     1.5     55.5        6      0.1
       0     55.5        6      0.1
    -0.5       54        6      0.1
    -2.5       55        6      0.1

    3 8
       4       58        6      0.3
     3.5     60.5        5      0.3
       4     64.5        6      0.3
     5.5     68.5        4      0.3
       6       72        4      0.3
     6.5       75      3.5      0.3
     6.5       78      3.5      0.3
     6.5       78      3.5      0.1

    2 4
     6.5       78      3.5      0.1
       6     80.5        4      0.1
       5       84        4      0.1
       6       89        4      0.1

    1 3
     6.5       78      3.5      0.1
       8       82      4.5      0.2
       9       85        4      0.2

    3 6
       9       85        4      0.2
    10.5       85        4      0.2
    11.5     88.5      4.5      0.2
    14.5     95.5        4      0.2
      15      100        4      0.2
      17    104.5        4      0.2

    3 5
       9       85        4      0.2
       9     88.5        4      0.2
       9       97        4      0.2
     9.5      105      4.5      0.2
     8.5    108.5      3.5      0.2

    1 3
       6        7      0.5        2
     6.5        9        4        2
     6.5     10.5      4.5        2

    3 8
     6.5     10.5      4.5        2
     8.5     10.5      4.5      0.8
       9        8      6.5      0.8
      10        4      6.5      0.8
    10.5       -2        8      0.8
    10.5       -4        8      0.8
      12       -6        8      0.8
    14.5     -6.5        8      0.8

    3 5
    14.5     -6.5        8      0.8
    16.5    -12.5       10      0.1
    15.5    -19.5       10      0.1
      14      -26     12.5      0.1
    11.5      -29     11.5      0.1

    3 8
    14.5     -6.5        8      0.8
    16.5       -3        9      0.2
    18.5        1      8.5      0.2
      20      3.5      8.5      0.2
    22.5        9        8      0.2
      25        8      5.5      0.2
    25.5        5        6      0.2
    27.5      5.5        6      0.2

    2 7
    27.5      5.5        6      0.2
      28        3        6      0.2
    30.5        3      5.5      0.2
    32.5      3.5      5.5      0.2
      33        3      5.5      0.2
      35      3.5        6      0.2
    38.5      4.5      7.5      0.2

    11 28
    27.5      5.5        6      0.2
    27.5      6.5      4.5      0.2
    29.5        8      4.5      0.2
      31        8      5.5      0.2
    33.5       14        4      0.2
      35     16.5        4      0.2
    37.5       22      4.5      0.2
    39.5     25.5      2.5      0.2
      42       28      5.5      0.2
      44     31.5      5.5      0.2
    47.5       32        4      0.2
      48     31.5        4      0.2
      49       27        2      0.2
    47.5       22        2      0.2
    51.5     20.5        2      0.2
    51.5       18      3.5      0.2
    51.5     15.5      3.5      0.2
    51.5       14      3.5      0.2
      53      9.5      3.5      0.2
      53        5        5      0.2
      56        3      4.5      0.2
      57        1      4.5      0.2
      59        1      5.5      0.2
      59     -3.5      6.5      0.2
    58.5       -8        6      0.1
      59    -15.5        6      0.1
      59      -23        6      0.1
    59.5      -27      5.5      0.1

    2 6
     6.5     10.5      4.5        2
     6.5     12.5        4      0.6
       9       15        4      0.6
    10.5       18        4      0.6
    10.5       24      3.5      0.6
      13     26.5      4.5      0.6

    2 7
      13     26.5      4.5      0.6
    13.5     28.5      4.5      0.1
    13.5     29.5      4.5      0.1
      12       30      3.5      0.1
      11     27.5      3.5      0.1
     8.5       22      3.5      0.1
       8     18.5      3.5      0.1

    5 11
      13     26.5      4.5      0.6
    14.5     27.5      4.5      0.1
    17.5       26      3.5      0.1
      19     27.5      6.5      0.1
      23     29.5      6.5      0.1
      25       32      5.5      0.1
      28     37.5        5      0.1
      32       43        4      0.1
    32.5       48        5      0.1
    32.5     52.5      2.5      0.1
    32.5     58.5      1.5      0.1


CONNECTIONS:
        0    1
        0    1


        0    1
        0    1
        2    1
        2    1
        4    1
        5    1
        5    1
        7    1
        7    1
        4    1
       10    1
       10    1

        0    1
        0    1
        2    1
        2    1

        0    1
        0    1
        2    1
        3    1
        4    1
        4    1
        6    1
        6    1
        8    1
        8    1
        3    1
        2    1
       12    1
       12    1
       14    1
       14    1
       16    1
       16    1
       18    1
       18    1

        0    1
        1    1
        1    1
        3    1
        3    1
        0    1
        6    1
        6    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")
}
.hoc file

Code: Select all

load_file("nrngui.hoc")
load_file("cts7259g.asc")

nSThcells=2
objectvar SThcells[nSThcells]

for i = 0, nSThcells-1 { 
	SThcells[i] = new CELL()
}

for i = 0, nSThcells-1 SThcells[i]{
	
	
	initseg {L=40}
	narrowr {L=90}
	axon {L=5340}

	initseg nseg=int(L/15)
	narrowr nseg=int(L/15)
	axon nseg=int(L/15)

	forall insert pas
	forall insert spike
	forall ena = 35.0
	forall ek = -75
	forall insert cad
	forall g_pas = .000008
	forall e_pas = -62.5
	forall Ra=110
	global_ra=110

	celsius=22

	for i = 0, 3-1 dend1[i] {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}
	dend2 {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}
	for i = 0, 13-1 dend3[i] {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}
	for i = 0, 5-1 dend4[i] {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}
	for i = 0, 21-1 dend5[i] {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}
	for i = 0, 9-1 dend6[i] {
	gcabar_spike = 0.002
	gkbar_spike = 0.012
	gabar_spike = 0.036
	gkcbar_spike = 0.000001
	gnabar_spike = 0.025
	}

	soma {
	diam=12.9168 
	gcabar_spike = 0.0015
	gkbar_spike = 0.018
	gabar_spike = 0.054
	gkcbar_spike = 0.000065
	gnabar_spike = 0.080
	}

	initseg {
	diam=1
	gcabar_spike = 0.0015
	gkbar_spike = 0.018
	gabar_spike = 0.054
	gkcbar_spike = 0.000065
	gnabar_spike = 0.150
	}

	narrowr {
	diam=0.4
	gcabar_spike = 0.0
	gkbar_spike = 0.018
	gabar_spike = 0.054
	gkcbar_spike = 0.000065
	gnabar_spike = 0.1
	}

	axon {
	diam=1
	gcabar_spike = 0.0
	gkbar_spike = 0.018
	gabar_spike = 0.0
	gkcbar_spike = 0.000065
	gnabar_spike = 0.070
	}


	connect soma(1),initseg(0)
	connect initseg(1),narrowr(0)
	connect narrowr(1),axon(0)
}
	
	
objectvar clamp
nSThcells[1].soma clamp = new IClamp(0.5)
// clamp.del = 0
// clamp.dur = 400
// clamp.amp = 0.01

load_proc("nrnmainmenu")
access nSThcells[1].soma

// xopen("test.ses")

init()
forall depth_cad = diam / 2
init()

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