/*----------------------------------------------------------------
%W% %G%
ri18um.dat1 translated Fri Jun 30 17:21:51 1995 by ntscable 2.0
source file syntax: Nevin
output file syntax: CABLE
soma: diameter = 1 um length = 0.1 um area = 0.314159 um2
3 three-D points numbered 1-3
1 primary neurites
72 branches totaling 8066.41 um in length, 28817.1 um2 in area
1092 tree points translated to 1531 segments (1 requested)
Neurites divided into segments of equal dx between adjacent digitized
points.
Segment length constrained to be < 10 um, or < 10 times
mean diameter of translation interval, whichever is less.
/*
ri18um.dat2, Cell Ri18
This file differs from its predecessor, ri18um.dat, in that the diameters
of the somatic points (18-31) have been multiplied by 0.77 to make the
circumference that of an ellipse (with a=2b) instead of a circle
coordinates and diameters in Nevin format
pt type x y z diam
--------------
Nelson's notes
--------------
-the compartment called soma is really part of the axon that was
reconstructed
-an additional axon is added to this "soma" by ntscable, and therefore
serves as an extension of the axon
-the reconstructed axon also includes dend1[0] to dend1[13]
-the real soma is dend1[14] to dend1[27]
-dend1[21] is the middle of the soma
-dend1[183] (beginning, ie, 0) is the dendritic recording location
----------------------------------------------------------------*//* make geometry explicit */
primary_branches_cell = 1
branches_cell = 72
max_dx_cell = 10
points_cell = 1092
nseg_cell = 1531double sections_cell[1]
sections_cell[0] = 1091
nsec_cell = 1093
strdef name_soma, name_section, name_axon
name_soma = "soma"
name_section = "dend"
name_axon = "axon"
use_axon = 1/* create sections */
create soma,\
axon,\
dend1[1091]
/*----------------------------------------------------------------*/
proc geometry() { local i, j
/* soma geometry */
soma {
nseg = 1
pt3dclear()
for j = 1, fscan() {
pt3dadd(fscan(),fscan(),fscan(),fscan())
}
}
/* axon geometry */
axon {
nseg = 1
pt3dclear()
pt3dadd(0,0,0,1e-4)
pt3dadd(0,0,1e-4,1e-4)
}
/* connect axon */
soma connect axon (0), 0.5/* connect primary neurites */
soma connect dend1[0] (0), 0.5/* neurite geometry*/for i = 0,1090 {
dend1[i] {
nseg = fscan()
pt3dclear()
for j = 1, fscan() {
pt3dadd(fscan(),fscan(),fscan(),fscan())
}
}
}
/* branching topology*/for i = 1,1090 {
dend1[fscan()] connect dend1[i] (0), fscan()
}
}
geometry()
SOMA COORDINATES AND DIAMETERS:
32.8-117.1212.8-117.12.0512.8-117.12.11
NEURITE COORDINATES AND DIAMETERS:
125.9-113.83.30.93.7-1083.31.3123.7-1083.31.34.6-10421.3124.6-10421.33.9-101.82.21123.9-101.82.215.1-96.92.21.2125.1-96.92.21.23.7-94.72.21223.7-94.72.214.6-82.42.21.1324.6-82.42.21.13.1-56.9-0.61.2223.1-56.9-0.61.2-0.2-45.1-0.61.312-0.2-45.1-0.61.3-0.7-37.31.41.312-0.7-37.31.41.30.1-33.92.61.5120.1-33.92.61.54.1-27.12.41.7124.1-27.12.41.74.7-18.12.42224.7-18.12.421-7.83.62.4121-7.83.62.40.2-7.50.73.23120.2-7.50.73.230.2-5.63.46.08120.2-5.63.46.080.2-3.63.49.24120.2-3.63.49.240.2-2.22.310.63120.2-2.22.310.630.204.114.55120.204.114.550.20.92.515.79120.20.92.515.790.23.80.419.17120.23.80.419.170.250.420.25120.250.420.250.260.419.1120.260.419.10.29.7116.86120.29.7116.860.214.42.113.17120.214.42.113.170.216.62.111.32120.216.62.111.320.219.52.18.7120.219.52.18.70.220.92.17.08120.220.92.17.080.222.92.17.6120.222.92.17.60.2292.17120.2292.17-0.534.73.45.612-0.534.73.45.6-1.93945.612-1.93945.6-0.445.44.8512-0.445.44.85-249.95.15.712-249.95.15.70.651.24.41.2120.651.24.41.23.654.54.91123.654.54.913.656.88.91123.656.88.910.757.88.60.8123.656.88.916.257.18.91126.257.18.916.259.37.51126.259.37.518.760.18.80.6128.760.18.80.611.458.211.20.61211.458.211.20.614.561.711.20.61214.561.711.20.621.162.8100.712-249.95.15.7-4.5595.25.112-4.5595.25.1-4.566.65.25.112-4.566.65.25.1-4.572.95.24.312-4.572.95.24.3-4.978.25.23.712-4.978.25.23.7-4.9834.6412-4.9834.64-8.984.90.31.412-8.984.90.31.4-15.584.5-1.31.312-15.584.5-1.31.3-19.288.6-2.91.212-19.288.6-2.91.2-24.390.2-2.91.412-24.390.2-2.91.4-27.694.7-9.11.512-27.694.7-9.11.5-34.594.7-6.11.622-34.594.7-6.11.6-34.5104.5-3.82.212-34.5104.5-3.82.2-35.7109.7-3.81.822-35.7109.7-3.81.8-43.5122.2-9.21.412-43.5122.2-9.21.4-48.3126.7-51.512-48.3126.7-51.5-51.6133.2-2.91.512-51.6133.2-2.91.5-54.8138.3-2.91.412-54.8138.3-2.91.4-56.2142.6-4.81.922-56.2142.6-4.81.9-64.3151-4.81.712-64.3151-4.81.7-66.4155.3-4.81.712-66.4155.3-4.81.7-66.4161.8-5.61.312-66.4161.8-5.61.3-68.9165.5-4.3122-68.9165.5-4.31-79.6167.600.912-79.6167.600.9-81.517200.922-81.517200.9-87.6183.6-3.20.812-87.6183.6-3.20.8-89.9188.1-4.60.612-89.9188.1-4.60.6-96.3193.3-3.80.522-96.3193.3-3.80.5-96.3205.1-1.90.722-4.9834.64-4.9954.63.522-4.9954.63.5-4.9110.12.53.512-4.9110.12.53.5-4.9112.12.53.522-4.9112.12.53.5-14.5109.33.21.612-14.5109.33.21.6-20.9111.12.71.322-20.9111.12.71.3-34.4106.15.91.112-34.4106.15.91.1-41.1103.46.80.912-41.1103.46.80.9-43.8103.78.30.912-43.8103.78.30.9-48.9102.98.30.812-48.9102.98.30.8-53.9100.85.31.112-53.9100.85.31.1-62.199.96.90.812-62.199.96.90.8-66.296.611.50.612-66.296.611.50.6-67.193.611.50.512-67.193.611.50.5-69.79711.50.612-4.9112.12.53.5-2.2119.32.53.712-2.2119.32.53.7-0.3122.80.6122-0.3122.80.618.5120.95.61.2128.5120.95.61.218.2122.65.10.81218.2122.65.10.824.7127.66.80.81224.7127.66.80.827.3133.66.80.81227.3133.66.80.830.8135.46.80.81230.8135.46.80.830.8138.17.411230.8138.17.4138.7139.47.71.11238.7139.47.71.148142.26.51.32248142.26.51.356.8142.412.30.91256.8142.412.30.960.11457.50.91260.11457.50.962.2145.612.10.41262.2145.612.10.463.3144.713.60.41263.3144.713.60.469.1143.213.30.41269.1143.213.30.470.1147.413.40.71270.1147.413.40.777.4142.717.40.61277.4142.717.40.679142.717.40.61248142.26.51.353.7138.39.60.71253.7138.39.60.759.3139.910.912259.3139.910.9169132.511.40.92269132.511.40.974.8125.48.40.62274.8125.48.40.681.6118.45.60.512-2.2119.32.53.7-2.2125.623.912-2.2125.623.9-0.3130.423.732-0.3130.423.7-5.8152.42.93.322-5.8152.42.93.3-1.5162.94.93.612-1.5162.94.93.61.51694.24.2121.51694.24.21.51694.11.2121.51694.11.2-3.6172.24.20.822-3.6172.24.20.8-11.1179.1-1.31.112-11.1179.1-1.31.1-13.6177-1.31.112-13.6177-1.31.1-16183.7-2.3122-16183.7-2.31-22.6190.3-7.4132-22.6190.3-7.41-42.3205.3-11.8122-42.3205.3-11.81-53.3205.3-150.922-53.3205.3-150.9-69.5207.6-16.70.912-11.1179.1-1.31.1-6.5180.5-0.6112-6.5180.5-0.61-7.2183.3-3.9112-7.2183.3-3.91-3.9185.7-6122-3.9185.7-61-6.4195.8-4.70.9121.51694.24.24.9173.35.43.2224.9173.35.43.2-1.5188.44.63.212-1.5188.44.63.21182.15.91121182.15.912.8178.56.41122.8178.56.417.6171.54.61.1127.6171.54.61.15.4166.44.61.1225.4166.44.61.19.4155.231229.4155.2315.8145.72.51225.8145.72.5112.9135.9-1.111212.9135.9-1.1114.2129.12.912214.2129.12.9110.7115.73.71.12210.7115.73.71.113.2105.35.70.91213.2105.35.70.99.5106.25.70.8229.5106.25.70.88.796.37.80.8128.796.37.80.86.792.911.70.7126.792.911.70.70.688.713.60.6120.688.713.60.60.687.213.60.6122.8178.56.416.9171.23.91126.9171.23.9113.5168.42.90.81213.5168.42.90.820.5168.41.61.21220.5168.41.61.225.7165.74.112225.7165.74.1129.1152.66.50.61225.7165.74.1134.9164.94.11.11234.9164.94.11.139.2166.66.811239.2166.66.8142.8160.96.811242.8160.96.8148.6159.96.80.91248.6159.96.80.952.8154.17.90.91252.8154.17.90.957.3151.47.90.91257.3151.47.90.959.4144.25.211259.4144.25.2162142.75.212262142.75.2167.3131.80.30.62267.3131.80.30.673.4119.4-0.60.62273.4119.4-0.60.682.1111.7-0.60.62282.1111.7-0.60.694101.7-0.80.612-1.5188.44.63.2-1.5189.84.63.222-1.5189.84.63.2-4.4199.53.13.412-4.4199.53.13.41.5201.6-0.60.8121.5201.6-0.60.8-0.2208.3-4.80.832-4.4199.53.13.4-8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22-111.3-146.2-2.30.8-115.6-151.92.40.812-115.6-151.92.40.8-114.8-154.53.50.522-114.8-154.53.50.5-121.1-1587.40.522-121.1-1587.40.5-130.1-162.510.60.512-130.1-162.510.60.5-132.3-160.810.60.522-132.3-160.810.60.5-134.2-169.210.30.412-134.2-169.210.30.4-134.8-169.210.30.5120.2-3.63.49.247.1-5.83.42127.1-5.83.4211-4.53.422211-4.53.4211-12.210.321211-12.210.3216.9-16.510.32220.2-5.63.46.08-0.5-17.93.41.712-0.5-17.93.41.7-5.7-19.83.41.722-5.7-19.83.41.7-16.3-28.34.41.612-16.3-28.34.41.6-16.7-29.810112-16.7-29.8101-13.8-29.8100.812-13.8-29.8100.8-14.4-32.6100.812-14.4-32.6100.8-22.4-33.2100.812-22.4-33.2100.8-30.7-38.212.40.5120.2-7.50.73.231.6-10.18.42121.6-10.18.42-6.4-10.18.41.212-6.4-10.18.41.2-11.5-16.48.40.612-11.5-16.48.40.6-14.4-19.19.50.622-14.4-19.19.50.6-24.9-149.50.612-24.9-149.50.6-31.2-18.59.50.822-31.2-18.59.50.8-40.5-24.79.50.812-40.5-24.79.50.8-43.7-319.50.812-43.7-319.50.8-46.2-31.29.50.812-46.2-31.29.50.8-48.2-28.54.60.822-48.2-28.54.60.8-62.8-33.74.6112-62.8-33.74.61-66-39.54.61.112-66-39.54.61.1-70.6-42.64.61.122-70.6-42.64.61.1-81.4-45.44.61.112-81.4-45.44.61.1-81.4-43.581.112-81.4-43.581.1-83.9-39.580.512-83.9-39.580.5-89.9-35.380.512-81.4-43.581.1-85.8-47.53.90.612-85.8-47.53.90.6-91.4-47.58.20.722-91.4-47.58.20.7-98.5-51.88.20.712-98.5-51.88.20.7-104.9-50.28.20.722-104.9-50.28.20.7-113.7-569.30.712-113.7-569.30.7-118.1-54.99.30.722-113.7-569.30.7-122.2-59.16.10.5
CONNECTIONS:
01112131415161718191101111121131141151161171181191201211221231241251261271281291301311321331341351351371381391401411321431441451461471481491501511521531541551561571581591601611621631641651661671681691471711721731741751761771781791801811821831731851861871881891901911921931941951961971981991100110119411031104110511061851108110911101111111211131114111511161117111811191120111511221123112411121126112711281129113011311132113311341135113611371138113911401141112911431144114511461146114811491150115111521153115411551156115711581127116011611162116111641165116611671168116911651171117211731174117511761177117811791180118111821183118411851186118711881189119011911192119311941195118811971198119912001201120212031204120512061207120812091210121112121213121412151216121712181219122012211222122312241225122612271228122912301227123212331234123512361237123812391240124112031243124412451246124612481249125012511252125312521255125611991258125912601261126212631264126512661267126812691270127112721273127412751276127712781279128012811282128312841285128612871288128912901291129212931294129512961297129812991300130113011303130413051306130713081309129713111312131313141287131613171318131913201321132213231324132513251327132813291329133112661333133413351336133713381339134013411342134313441345134613471348134913501351135213531354135513561357135813591360136113601363136413651366136713381369137013711372137313741375137613771378137913801381138213831384138513861387138813891390139113911386139413951396139713981399140014011402140314041184140614071408140914101411141214131414141514161417141814191420142114221423142414251426142714281429143014311432143314341435143614371438143914401441144214431444144514461447144814491450145114481453145414551456145714581459146014381462146314641465146614671468146914701471147214731474147514761477147814251480148114821483148414851486148714881489149014911492149314941495149614971498149915001501150215031504148915061507150815091510151115121513151415151516151715181519152015211522152315241525151415271528152915301531153215331534153515361537153815391407154115421543154415451546154715481549155015511552155315541555155615571558155915601561156215631564156515661567156815691570157115721573157415751576157715781579158015811582158315841585158615871588158915901591159215931594157515961597159815991600160116021603160416051606160716081609161016111612161316141615161616171618161916201621162216231624162516261627162816291630163116321633163415611636163716381639164016411642164316441645164616471648164916501651165216531654165516561657165816591660166116621663166416651666166716681669167016711672167316741675167616771678167916801681168216831684168516411687168816891690169116921693169416901696169716981699170017011702170317041705170617071708170917101711171217131714171517161717171817191720172117221723172417251726172717281729173017311732173317341735173617371738173917301741174217431744174517461747172817491750175117521753175417551756175717581301760176117621763176417651766176717681769177017711761177317741775121177717781779178017811782178317841785178617871788178917901791178417931794179517961797179817831800180118021803180418051806120180818091810181118121813181418151816181118181819182018211822182318241825182618271828182918301831182518331834182118361837183818391840184118421843184418451846184718481849185018511852185318541855185618571858185918601861186218631864186518181867186818691870187118721873187418751876187718771879188018101882188318841885188618871888188918901891189218931894189518961897189818931900190119021903190419051906190019081909191019111912191319141915191619171918191919201921119192319241925192619241928192919301928193219331934193519361937193819391940194119421943193519451946194719481949195019511952195319541955118195719581959196019611962196319641965196619671968196919701971197219731974197519761963197819791980198119821983198419851986198719881989199019911992199319941994198519971998199911000110011100211003110041161100611007110081100911010110111101211013110141101511016110171101811019110201102111022110231102411025110261102711028110291103011031110321103311019110351103611037110381103911040110411104211043110441104511046110471104811049110501105111052110531151105511056110571141105911060110611106211063110641106511311067110681106911070110711107211073110741107511076110771107811079110801108111082110811108411085110861108711088110881
proc correct() {
/* correct diameters of dendrites at origins of basals */
dend1[777] {diam=1.40}
dend1[808] {diam=2.40}
dend1[923] {diam=1.40}
dend1[957] {diam=1.40}
dend1[1006] {diam=1.70}
dend1[1055] {diam=2.00}
dend1[1059] {diam=1.70}
dend1[1067] {diam=2.00}
/* correct diameters of dendrites at origins of obliques */
dend1[33] {diam=1.20}
dend1[48] {diam=1.35}
dend1[74] {diam=1.60}
dend1[86] {diam=2.45}
dend1[113] {diam=0.80}
dend1[128] {diam=1.00}
dend1[162] {diam=0.80}
dend1[760] {diam=1.30}
/* increase number of segments for somatic compartments */for i=14,27 {
dend1[i] {nseg=10}
}
}
correct()
/*----------------------------------------------------------------*/
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")
}