Import3D creates 2 soma
Posted: Mon Oct 17, 2011 11:57 am
Hello, I am importing a 3d morphology using the Import 3D tool. When I import I get an error:
Main branch starting at line 657 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
I then get a "Possible root branch errors" dialog box that says"
Default logical connection to nearest soma.
Check to physically connect to closest parent in the xy plane.
(Note: may split the parent into two sections)
If I select this option it does create a soma[1](0) and a soma(1) in the .hoc code both of which have many pt3dadd entries with in them:
At the bottom of the exported .hoc file it creates a somatic section list.
the topology section look like:
I am not sure why the soma gets split into two or the implications of this. Do the two somatic sections still act as one large soma? or are they somehow more isolated?
Main branch starting at line 657 is outside the soma bounding boxes
Making a logical connection to center of nearest soma
I then get a "Possible root branch errors" dialog box that says"
Default logical connection to nearest soma.
Check to physically connect to closest parent in the xy plane.
(Note: may split the parent into two sections)
If I select this option it does create a soma[1](0) and a soma(1) in the .hoc code both of which have many pt3dadd entries with in them:
Code: Select all
proc shape3d_1() {
soma {pt3dclear()
pt3dadd(-1.47, 1.1, 0, 0.18)
pt3dadd(-1.47, 1.65, 0, 0.18)
pt3dadd(-1.65, 2.2, 0, 0.18)
pt3dadd(-2.02, 2.75, 0, 0.18)
pt3dadd(-2.39, 3.49, 0, 0.18)
pt3dadd(-2.75, 4.22, 0, 0.18)
pt3dadd(-3.86, 5.51, 0, 0.18)
pt3dadd(-4.59, 6.61, 0, 0.18)
pt3dadd(-5.51, 7.53, 0, 0.18)
pt3dadd(-6.43, 8.81, 0, 0.18)
pt3dadd(-6.98, 9.73, 0, 0.18)
pt3dadd(-7.71, 10.83, 0, 0.18)
pt3dadd(-8.81, 12.67, 0, 0.18)
pt3dadd(-10.1, 14.5, 0, 0.18)
pt3dadd(-11.01, 16.16, 0, 0.18)
pt3dadd(-11.2, 17.44, 0, 0.18)
pt3dadd(-11.2, 21.3, 0, 0.18)
pt3dadd(-10.65, 23.13, 0, 0.18)
pt3dadd(-10.1, 23.68, 0, 0.18)
pt3dadd(-9.55, 23.87, 0, 0.18)
pt3dadd(-7.89, 24.42, 0, 0.18)
pt3dadd(-6.79, 24.78, 0, 0.18)
pt3dadd(-5.69, 25.15, 0, 0.18)
pt3dadd(-3.49, 25.15, 0, 0.18)
pt3dadd(-2.75, 24.97, 0, 0.18)
pt3dadd(-2.02, 24.42, 0, 0.18)
}
soma[1] {pt3dclear()
pt3dadd(1.85504, 0.69267, 0, 0.925963)
pt3dadd(1.70518, 1.87436, 0, 1.42094)
pt3dadd(1.55533, 3.05605, 0, 1.5322)
pt3dadd(1.40547, 4.23773, 0, 1.3983)
pt3dadd(1.25562, 5.41942, 0, 1.35015)
pt3dadd(1.10576, 6.60111, 0, 1.49653)
pt3dadd(0.955908, 7.7828, 0, 1.50179)
pt3dadd(0.806054, 8.96448, 0, 1.33946)
pt3dadd(0.656199, 10.1462, 0, 1.03173)
pt3dadd(0.506345, 11.3279, 0, 0.832381)
pt3dadd(0.35649, 12.5095, 0, 0.69106)
pt3dadd(0.206636, 13.6912, 0, 0.4867)
pt3dadd(0.0567811, 14.8729, 0, 0.522405)
pt3dadd(-0.0930734, 16.0546, 0, 0.673459)
pt3dadd(-0.242928, 17.2363, 0, 1.13828)
pt3dadd(-0.392782, 18.418, 0, 1.46059)
pt3dadd(-0.542637, 19.5997, 0, 1.68103)
pt3dadd(-0.692491, 20.7814, 0, 1.78193)
pt3dadd(-0.842346, 21.963, 0, 1.5043)
pt3dadd(-0.9922, 23.1447, 0, 1.17581)
pt3dadd(-1.14205, 24.3264, 0, 0.804093)
}
At the bottom of the exported .hoc file it creates a somatic section list.
Code: Select all
somatic = new SectionList()
for i=0, 1 soma[i] somatic.append()
Code: Select all
proc topol() { local i
connect soma[1](0), soma(1)
connect dend(0), soma[1](0.5)
for i = 1, 2 connect dend[i](0), dend(1)
for i = 3, 4 connect dend[i](0), dend[2](1)
connect dend[5](0), soma[1](0.5)
connect dend[6](0), soma(1)
for i = 7, 8 connect dend[i](0), dend[i-1](1)
connect dend[9](0), dend[7](1)
connect dend[10](0), dend[6](1)
for i = 11, 12 connect dend[i](0), dend[10](1)
for i = 13, 14 connect dend[i](0), soma[1](0.5)
for i = 15, 16 connect dend[i](0), dend[i-1](1)
connect dend[17](0), dend[15](1)
connect dend[18](0), dend[14](1)
connect dend[19](0), soma[1](0.5)
for i = 20, 21 connect dend[i](0), dend[19](1)
for i = 22, 23 connect dend[i](0), dend[21](1)
connect apic(0), soma[1](0.5)
for i = 1, 2 connect apic[i](0), apic[i-1](1)
connect apic[3](0), apic[1](1)
connect apic[4](0), apic(1)
for i = 5, 7 connect apic[i](0), apic[i-1](1)
connect apic[8](0), apic[6](1)
for i = 9, 10 connect apic[i](0), apic[8](1)
connect apic[11](0), apic[5](1)
for i = 12, 13 connect apic[i](0), apic[11](1)
connect apic[14](0), apic[4](1)
for i = 15, 16 connect apic[i](0), apic[i-1](1)
connect apic[17](0), apic[14](1)
for i = 18, 19 connect apic[i](0), apic[i-1](1)
connect apic[20](0), apic[18](1)
connect apic[21](0), apic[17](1)
connect apic[22](0), soma[1](0.5)
for i = 23, 24 connect apic[i](0), apic[i-1](1)
connect apic[25](0), apic[23](1)
for i = 26, 27 connect apic[i](0), apic[i-1](1)
connect apic[28](0), apic[26](1)
connect apic[29](0), apic[25](1)
connect apic[30](0), apic[22](1)
basic_shape()
}