Retinal ganglion cells responses and activity (Tsai et al 2012, Guo et al 2016)

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Accession:260653
From the abstracts: "Retinal ganglion cells (RGCs), which survive in large numbers following neurodegenerative diseases, could be stimulated with extracellular electric pulses to elicit artificial percepts. How do the RGCs respond to electrical stimulation at the sub-cellular level under different stimulus configurations, and how does this influence the whole-cell response? At the population level, why have experiments yielded conflicting evidence regarding the extent of passing axon activation? We addressed these questions through simulations of morphologically and biophysically detailed computational RGC models on high performance computing clusters. We conducted the analyses on both large-field RGCs and small-field midget RGCs. ...", "... In this study, an existing RGC ionic model was extended by including a hyperpolarization activated non-selective cationic current as well as a T-type calcium current identified in recent experimental findings. Biophysically-defined model parameters were simultaneously optimized against multiple experimental recordings from ON and OFF RGCs. ...
References:
1 . Guo T, Tsai D, Morley JW, Suaning GJ, Kameneva T, Lovell NH, Dokos S (2016) Electrical activity of ON and OFF retinal ganglion cells: a modelling study. J Neural Eng 13:025005 [PubMed]
2 . Tsai D, Chen S, Protti DA, Morley JW, Suaning GJ, Lovell NH (2012) Responses of retinal ganglion cells to extracellular electrical stimulation, from single cell to population: model-based analysis. PLoS One 7:e53357 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Extracellular;
Brain Region(s)/Organism: Retina;
Cell Type(s): Retina ganglion GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Activity Patterns; Development;
Implementer(s): Tsai, David [d.tsai at unsw.edu.au];
Search NeuronDB for information about:  Retina ganglion GLU cell;
/*----------------------------------------------------------------
%W%  %G%
ctt3219m.asc  translated Tue Dec 17 10:29:44 1996 by ntscable 2.0
source file syntax: Eutectic
output file syntax: CABLE
soma: diameter = 11.6502 um  length = 21.752 um  area = 796.125 um2
      13 three-D points; 14 outline points numbered 1-14
      outline diameter = 17.0615 um
3 primary neurites
28 branches totaling 1755.23 um in length, 5409.43 um2 in area
482 tree points translated to 202 segments (1 requested)
Neurites divided into segments of equal dx between adjacent digitized
branch points.
Segment length constrained to be < 10 um.
No. points    496
No. trees       4
Text  CTT3219M.GR1                                                                                                            

----------------------------------------------------------------*/
					/* create sections */
create    soma,\
          dend1[33],\
          dend2[19],\
          ah[1]



/*----------------------------------------------------------------*/
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 ah[0] (0), 0.5


					/* neurite geometry*/
    for i = 0,32 {
        dend1[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

    for i = 0,18 {
        dend2[i] {
            nseg = fscan()
            pt3dclear()
            for j = 1, fscan() {
                pt3dadd(fscan(),fscan(),fscan(),fscan())
            }
        }
    }

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



					/* branching topology*/
    for i = 1,32 {
        dend1[fscan()] connect dend1[i] (0), fscan()
    }

    for i = 1,18 {
        dend2[fscan()] connect dend2[i] (0), fscan()
    }

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

}

geometry()


SOMA COORDINATES AND DIAMETERS:

    13
    -9.5        2      2.5        0
    -8.5        1    1.125   6.1288
    -8.5      0.5    1.125   7.1107
    -7.5    0.625     0.75   10.762
    -6.5     0.15     0.65   13.303
      -5  0.32143  0.39286   15.359
      -3 -0.41667        0   16.167
     0.5  -1.2083  -1.1875   16.595
       1  -1.1429    -1.25   16.293
       4 -0.83333    -1.25   14.342
     5.5     0.25       -1     11.5
       8  0.83333 -0.83333   4.5338
     8.5     -0.5        0        0


NEURITE COORDINATES AND DIAMETERS:

    4 5
    -2.5      8.5        0      7.2
       4     10.5        8      4.8
      10       12       11      5.6
      17       12       11      5.6
    26.5       13       12      5.6

    2 5
    26.5       13       12      5.6
    29.5     16.5     13.5      3.7
    34.5     20.5       12      4.3
    39.5     22.5       12      5.1
    41.5       23     12.5      4.3

    1 2
    41.5       23     12.5      4.3
      46       21       14      4.3

    2 4
      46       21       14      4.3
    50.5     17.5     14.5      2.9
      56       17     15.5      3.9
      56       17     15.5      3.9

    2 5
      56       17     15.5      3.9
      60     17.5       14      2.2
      66       20     11.5      1.4
    70.5       20       13      1.4
    72.5       21       13      1.4

    1 4
    72.5       21       13      1.4
    74.5       18     12.5      0.1
      75     15.5     12.5      0.1
      75     15.5     12.5      0.1

    3 9
    72.5       21       13      1.4
    74.5     22.5     13.5      1.3
      77     23.5     13.5      1.3
    79.5     22.5       13      1.3
      84     22.5       13      1.1
      88     21.5       12      1.1
    91.5     20.5       12      1.1
    94.5       20     12.5      1.1
    96.5     19.5       12      1.5

    2 6
    96.5     19.5       12      1.5
      98     17.5     12.5      0.1
     101     13.5       13      0.1
   104.5     10.5       13      0.1
     107        9       11      0.1
   110.5        8       11      0.1

    10 26
    96.5     19.5       12      1.5
    99.5     20.5     13.5      1.1
     103     22.5       13      1.1
     106     23.5       12      1.1
     107       24       12      1.1
   109.5       26     12.5      1.1
   111.5       26     12.5      1.1
   115.5       30       14      1.1
     118     29.5     13.5      1.1
     123     32.5     14.5      1.1
   124.5       34     13.5      0.9
     127     34.5       15      0.9
   131.5     37.5       16      0.9
   134.5       39     16.5      0.9
     138       41       14        1
   142.5       42     12.5        1
   146.5       42     13.5        1
     149       44     13.5        1
     153     44.5       14        1
   156.5     45.5     14.5        1
   163.5       46     14.5        1
     166       48     13.5        1
   170.5     47.5       13      0.8
   172.5     48.5       12      0.8
     175       46       12      0.8
   179.5       44       13      1.1

    3 9
   179.5       44       13      1.1
   182.5     43.5     13.5      0.3
     185       44     13.5      0.3
   187.5     43.5       12      0.3
   190.5     41.5       12      0.3
     194       38       12      0.1
   196.5     36.5       12      0.1
   199.5     36.5       12      0.1
     202     36.5       12      0.1

    3 11
   179.5       44       13      1.1
   178.5     42.5     13.5      0.3
   179.5     38.5       12      0.4
   181.5       36       13      0.4
   183.5       34     12.5      0.4
   184.5       32     12.5      0.4
   186.5     30.5     12.5      0.4
     189     27.5     12.5      0.4
   188.5       26       12      0.1
   189.5       23     12.5      0.1
     189     21.5      9.5      0.1

    3 7
      56       17     15.5      3.9
    56.5     13.5     16.5      1.6
      60     10.5     15.5      1.6
      64        9       15      1.9
      66      6.5     14.5      1.9
    70.5      5.5     13.5      1.9
      72      3.5     16.5      1.9

    2 6
      72      3.5     16.5      1.9
      70        0     16.5      0.1
    69.5       -4       17      0.1
    66.5     -4.5       17      0.1
    66.5       -8       17      0.1
    63.5     -9.5       17      0.1

    11 27
      72      3.5     16.5      1.9
      74        1     14.5      1.1
    76.5     -0.5       14      1.1
    80.5     -2.5       14      1.1
      84     -4.5       12      1.9
    87.5     -6.5       13      1.7
      90     -7.5       12      1.7
      94     -6.5       13      1.3
    96.5       -6     13.5      1.3
    99.5     -6.5       15      1.3
     104       -5       15      1.3
   109.5       -4     15.5      1.3
   112.5     -3.5     16.5      1.3
     116      0.5     16.5      1.3
     119      1.5     15.5      1.7
   122.5      5.5     17.5      1.7
   125.5      5.5       16      1.7
   131.5      5.5     15.5      1.7
   134.5      4.5       14      1.7
     137      4.5     14.5      1.7
     140        4     12.5      1.7
     142        3       13      1.7
   146.5      2.5       12      1.7
   150.5      0.5       11      1.7
   153.5        0       11      5.3
   159.5     -1.5       11      0.1
   159.5     -1.5       11      0.1

    1 3
      46       21       14      4.3
    47.5     22.5     14.5      2.2
      50       24     14.5      1.7

    10 21
      50       24     14.5      1.7
      55       23       13      0.3
    61.5       25     12.5      0.3
    66.5       28       12      0.3
    68.5       29       12      0.1
    70.5     31.5       12      0.1
      74     34.5       12      0.1
      76       35     12.5      0.1
    78.5     37.5     10.5      0.1
      82     40.5     10.5      0.1
      85       42     10.5      0.1
      87     43.5     10.5      0.1
      90       49     10.5      0.1
      91       51     10.5      0.1
    94.5       53       11      0.1
    99.5       55     11.5      0.1
   103.5     55.5     11.5      0.1
   108.5       60     10.5      0.1
     112     62.5     10.5      0.1
   116.5       65     10.5      0.1
     123       70     10.5      0.1

    1 4
      50       24     14.5      1.7
    52.5       26       17        1
      53       28     17.5        1
      54     29.5     18.5        1

    1 4
      54     29.5     18.5        1
      55       32       19      0.1
      55       36       16      0.1
    54.5     37.5       16      0.1

    2 4
      54     29.5     18.5        1
      56       30       17      0.7
    59.5     31.5     17.5      0.7
    61.5     34.5     15.5      0.7

    2 5
    61.5     34.5     15.5      0.7
      61     36.5     15.5      0.1
      59       39     15.5      0.1
      58       44     15.5      0.1
    58.5       44     15.5      0.1

    5 13
    61.5     34.5     15.5      0.7
      64       36     14.5      0.7
    67.5       39       13      0.7
    69.5     40.5     12.5      0.7
    73.5     42.5     13.5      0.7
    76.5       44     13.5      0.7
      78     47.5       13      0.7
      81     48.5     13.5      0.7
      82     52.5       14      0.7
    84.5     55.5     12.5      1.2
    84.5     57.5       12      0.7
    87.5     59.5       12      0.7
      89     61.5       12      1.4

    4 9
      89     61.5       12      1.4
      88       64       11      0.1
      87     66.5      9.5      0.1
    91.5     69.5     11.5      0.1
    94.5     71.5     10.5      0.1
    96.5     75.5     10.5      0.1
    98.5     78.5     10.5      0.1
     100       81       11      0.1
   102.5     83.5       11      0.1

    10 26
      89     61.5       12      1.4
      92     61.5     11.5      0.6
      96       63     13.5      0.6
    99.5     63.5       11      0.6
     102       64       13      0.6
   104.5       66       11      0.8
   108.5     66.5       13      0.8
     110       70     12.5      0.8
   114.5       70     12.5      0.6
     117     71.5       14      0.6
   120.5     72.5       13      0.4
     124       73       13      0.4
   127.5       75       13      0.4
   130.5       76       13      0.4
   134.5       79       13      0.4
     139     79.5       13      0.4
   142.5     78.5       13      0.4
   145.5       80       13      0.4
   148.5       81       14      0.2
     151     83.5       14      0.2
   153.5       84       14      0.2
   157.5       82     14.5      0.2
     160       80       14      0.2
     163       79       15      0.2
     165     77.5     14.5      0.2
     168     76.5       13      0.1

    9 24
    41.5       23     12.5      4.3
      42     24.5       13      1.4
      44     29.5       13      1.4
    46.5     29.5     13.5      1.4
    48.5     29.5     13.5      1.4
    51.5       32     14.5      1.4
      55     33.5       14      1.1
      57       35       14      1.1
    60.5       36     12.5      1.1
    62.5       38     12.5      1.1
    65.5     38.5     12.5      1.1
      69       42     10.5      1.1
      71       43       11      1.1
    73.5       47       11      1.1
      72     51.5       11      1.1
      72       53       11      1.1
    73.5     56.5     12.5      1.1
      71       60       12      1.1
      72     65.5       12      1.1
    71.5     67.5     14.5      1.1
    72.5       70     14.5      1.1
      72     72.5     14.5      1.1
      74       75       13      1.1
      73     78.5       13      1.1

    1 3
      73     78.5       13      1.1
      72       80     13.5      0.4
      72       81       13      0.4

    2 5
      72       81       13      0.4
    72.5     83.5     13.5      0.1
      73     86.5     13.5      0.1
      74     89.5       14      0.1
    74.5     92.5       14      0.1

    7 22
      72       81       13      0.4
      70       82       14      0.6
      68       83     13.5      0.6
      67       85       13      0.6
      66       88       14      0.4
      63       89     14.5      0.4
      63     91.5     15.5      0.4
    64.5     94.5       15      0.4
      63     99.5     16.5      0.4
      65    103.5     16.5      0.4
      65      106       17      0.4
      67    108.5       17      0.4
    65.5    111.5       17      0.4
    67.5      114       17      0.4
    66.5      116       17      0.4
      68    117.5       17      0.4
    67.5      120       18      0.4
      69      122       18      0.4
      68    125.5     18.5      0.4
      71      129     19.5      0.4
      73      134     17.5      0.4
      73      134     17.5      0.1

    1 3
      73      134     17.5      0.1
      75    134.5     17.5      0.1
      76      136     17.5      0.1

    1 3
      73      134     17.5      0.1
      72    135.5     17.5      0.1
    71.5    137.5     17.5      0.1

    10 30
      73     78.5       13      1.1
    75.5       81     12.5      0.4
      78     84.5       13      0.4
      79       89       11      0.7
    77.5       93     11.5      0.7
      80       95       11      0.7
      81     98.5       12      0.7
      82    100.5       13      0.7
    81.5    103.5       13      0.5
    84.5      105       14      0.5
    85.5    108.5     14.5      0.5
      87      110     14.5      0.4
    87.5      113     14.5      0.4
    89.5      116     14.5      0.4
    91.5    117.5       14      0.4
      93      121       14      0.5
      95      123       14      0.5
      97      124       14      0.5
    97.5    126.5     15.5      0.5
    98.5      130     14.5      0.5
   100.5    130.5     14.5      0.5
   103.5      134       13      0.5
   105.5      134       13      0.5
     107    137.5       12      0.5
     111    138.5       12      0.5
     113      142       12      0.5
     117    143.5     13.5      0.5
     120    145.5     13.5      0.5
     123      147     13.5      0.5
   124.5      149     13.5      0.5

    1 4
   124.5      149     13.5      0.5
     126    148.5     13.5      0.3
     128    149.5       14      0.3
     128    150.5       14      0.3

    1 4
   124.5      149     13.5      0.5
     124    150.5       13      0.1
   125.5      152       13      0.1
   125.5      152       13      0.1

    5 13
    26.5       13       12      5.6
    28.5       11     15.5      0.4
      31     10.5       14      0.4
    32.5      6.5     12.5      0.6
    36.5        4     12.5      0.6
    38.5      2.5       14      0.4
      42        2     12.5      0.4
    45.5        1       14      0.4
    51.5      0.5     13.5      0.4
      56        0     12.5      0.4
      61        0     15.5      0.2
    64.5     -1.5       14      0.2
    65.5       -3       14      0.1

    2 3
    -5.5      7.5        0      4.7
      -7       12      7.5      4.7
    -9.5       17     10.5      5.3

    3 7
    -9.5       17     10.5      5.3
    -7.5       20     10.5      2.2
      -2     23.5       12      2.2
       1     27.5     14.5      2.2
     2.5       31     14.5      2.2
       6     34.5     15.5      2.2
     9.5       37       16      2.2

    8 19
     9.5       37       16      2.2
      14     37.5       16      0.4
    19.5       39       15      0.4
    23.5     39.5     13.5      0.4
    26.5     42.5       14      0.4
      30     44.5       14      0.4
    31.5       45       14      0.4
    34.5     47.5     12.5      0.3
    36.5       49     13.5      0.3
    41.5       51       13      0.1
    45.5     53.5     13.5      0.1
    49.5       54     13.5      0.1
      53       56     13.5      0.1
    57.5       57     13.5      0.1
    60.5     58.5       13      0.1
      63     60.5       13      0.1
      66     62.5     13.5      0.1
      69     65.5     13.5      0.1
    70.5       68     14.5      0.1

    1 3
     9.5       37       16      2.2
       9     38.5     15.5      1.5
       9     40.5     15.5      1.5

    2 6
       9     40.5     15.5      1.5
       7     43.5     15.5      0.1
       7     46.5     15.5      0.1
       7       49     15.5      0.1
     7.5     55.5     16.5      0.1
     6.5     58.5     16.5      0.1

    15 35
       9     40.5     15.5      1.5
      11       44       17      1.4
    13.5     45.5       17      1.4
      15     46.5       17      1.1
    16.5     50.5       17      1.1
      19     52.5       17      1.1
      19     55.5     16.5      1.1
    22.5     59.5     16.5      1.1
      23     62.5       14      1.1
      26       66       14      1.1
    30.5     68.5       14      1.1
    30.5       71       14      1.1
    34.5     72.5       13      1.1
      35       76       13      1.1
      38       80       13      1.1
    39.5       81       13      1.1
    39.5       85     12.5      1.1
      45       88     12.5      1.1
    48.5       91       13      1.1
    55.5     92.5       14      1.1
    60.5       94       14      1.1
    66.5      100       13      1.1
    70.5    102.5     12.5        1
      73      104     11.5      1.1
      75    108.5       13      1.1
      75    111.5       15      1.1
      75      114       16      1.1
    73.5      117     14.5      1.1
      75      120     14.5      0.9
    73.5    122.5       14      0.9
    71.5    126.5       14      0.9
    72.5    130.5     13.5      0.9
    72.5    132.5     13.5      0.9
      77    135.5       17      0.9
    79.5      137       18      0.9

    1 5
    79.5      137       18      0.9
      81    136.5     17.5      0.2
      84    137.5     17.5      0.2
      84    138.5     17.5      0.2
      84    138.5     17.5      0.2

    1 5
    79.5      137       18      0.9
    79.5      138       18      0.2
    81.5      140     19.5      0.2
    83.5      140       19      0.2
      84    138.5       19      0.2

    2 6
    -9.5       17     10.5      5.3
   -12.5       21     13.5      2.8
   -15.5       22       15      2.8
   -18.5     25.5       15      2.8
   -19.5     27.5       15      1.9
   -22.5       28     14.5      2.1

    1 3
   -22.5       28     14.5      2.1
     -26       27       17      0.4
   -28.5       27     16.5      0.2

    3 7
   -28.5       27     16.5      0.2
   -30.5       25     15.5      0.1
     -33     21.5       15      0.1
   -36.5     20.5       15      0.1
     -39     17.5       16      0.1
     -44     17.5       15      0.1
     -47       18     15.5      0.1

    4 10
   -28.5       27     16.5      0.2
     -30       28     15.5      0.2
     -32       29       16      0.2
   -36.5     27.5     16.5      0.2
   -41.5       26       16      0.2
     -47     27.5     16.5      0.2
   -52.5     29.5       16      0.2
   -56.5     31.5     17.5      0.2
     -64       36       16      0.1
     -64       36       16      0.1

    1 3
   -22.5       28     14.5      2.1
     -22     30.5     14.5      2.3
     -25       35       16      2.3

    10 30
     -25       35       16      2.3
   -23.5     37.5     16.5      0.5
   -22.5       40     15.5      0.5
   -21.5     41.5     15.5      0.8
     -21       44     15.5      0.6
     -18       46       17      0.6
   -16.5       47       17      0.6
   -15.5     50.5     15.5      0.5
     -14     52.5     15.5      0.5
   -11.5       54     15.5      0.5
   -10.5     56.5     15.5      0.5
     -10     58.5     15.5      0.5
     -11       60     15.5      0.5
   -10.5       63       15      0.5
     -11       65     16.5      0.5
   -10.5       68     15.5      0.5
   -10.5     71.5     16.5      0.5
    -7.5     74.5     18.5      0.4
      -6       77     19.5      0.4
    -5.5     79.5     21.5      0.4
      -3     81.5     19.5      0.4
    -1.5     85.5       21      0.4
       0     86.5       21      0.4
       3     87.5       21      0.4
     4.5     91.5       19      0.4
     5.5       95     17.5      0.4
     7.5       97       17      0.4
       7     99.5       16      0.4
       9    102.5     16.5      0.4
    10.5      108       17      0.4

    3 6
    10.5      108       17      0.4
       7      109       17      0.1
       4      110       17      0.1
     1.5    114.5     17.5      0.1
    -4.5    117.5     17.5      0.1
    -6.5    117.5     17.5      0.1

    3 10
    10.5      108       17      0.4
    12.5    110.5       16      0.3
      14      112     15.5      0.3
      15    115.5     15.5      0.3
    17.5      119       16      0.3
    17.5    121.5     16.5      0.3
    18.5      123       15      0.3
      18      126       15      0.3
      19    128.5     14.5      0.3
      19      131     14.5      4.5

    2 6
     -25       35       16      2.3
   -27.5     36.5       16      1.9
   -29.5     38.5     16.5      1.9
   -31.5       40       16      1.9
   -33.5       44     16.5      1.9
   -37.5     46.5     16.5      1.9

    4 13
   -37.5     46.5     16.5      1.9
   -37.5     50.5       17      0.1
     -39     53.5       17      0.1
     -42       54     17.5      0.1
     -42     57.5       15      0.1
     -44     59.5     14.5      0.1
   -43.5     62.5     14.5      0.1
     -45     63.5     14.5      0.1
     -45     64.5     14.5      0.1
   -47.5     66.5     14.5      0.1
   -48.5     69.5       15      0.1
   -49.5       74     15.5      0.1
     -52       78     15.5      0.1

    5 13
   -37.5     46.5     16.5      1.9
     -41       46       18      1.4
   -45.5       45       18      1.4
     -50     44.5       18      1.4
     -54       46       18      1.4
   -58.5       49     17.5      1.4
     -63       52     17.5      1.4
   -67.5     53.5     16.5      1.4
   -69.5       54     16.5      1.4
     -72       55       16      4.6
   -74.5     57.5       16      0.1
     -76     60.5       16      0.1
   -78.5       64       16      0.1

    7 16
       0      1.5        0      1.2
      -1     -0.5       -3      1.2
    -0.5     -3.5     -4.5      1.2
      -2     -7.5     -5.5      1.2
      -3    -13.5       -6      1.2
      -2    -16.5     -7.5      0.8
      -4      -20       -6      0.8
    -4.5    -21.5       -6      0.8
    -5.5    -24.5       -6      0.5
      -6      -29     -5.5      0.5
    -8.5      -35     -5.5      0.3
   -10.5      -38     -5.5      0.3
   -12.5      -41       -5      0.3
     -13      -48       -4      0.3
   -13.5    -50.5     -4.5      0.3
   -14.5    -52.5       -3      0.1


CONNECTIONS:
        0    1
        1    1
        2    1
        3    1
        4    1
        4    1
        6    1
        6    1
        8    1
        8    1
        3    1
       11    1
       11    1
        2    1
       14    1
       14    1
       16    1
       16    1
       18    1
       18    1
       20    1
       20    1
        1    1
       23    1
       24    1
       24    1
       26    1
       26    1
       23    1
       29    1
       29    1
        0    1

        0    1
        1    1
        1    1
        3    1
        3    1
        5    1
        5    1
        0    1
        8    1
        9    1
        9    1
        8    1
       12    1
       13    1
       13    1
       12    1
       16    1
       16    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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