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Neuron SWC import3d
1 1 0 0 0 10 -1
Generates a soma with length=20 and diam=20
1 1 0 0 -10 10 -1
2 1 0 0 0 10 1
Generates a soma with length=10 and diam=20
1 1 0 0 -20 5 -1
2 1 0 0 0 8 1
Generates a soma with length=20 and diam=13
1 1 0 0 -10 10 -1
2 1 0 0 0 10 1
3 1 0 0 10 10 2
Generates a soma with length=20 and diam=20
1 1 0 0 -5 2 -1
2 1 0 0 0 5 1
3 1 0 0 10 4 2
Generates a soma with length=15 and diam=8.3333
1 1 0 0 0 10 -1
2 1 0 0 -10 10 1
3 1 0 0 10 10 1
Generates a soma with length=20 and diam=20 - BUT the following warnings are generated:
One point section Import3d_Section[2] ending at line 3 has been removed
One point section Import3d_Section[1] ending at line 2 has been removed
1 1 0 0 0 10 -1
2 1 0 0 -4 6 1
3 1 0 0 1 0.5 1
Generates a soma with length=20 and diam=20 - BUT the following warnings are generated:
One point section Import3d_Section[2] ending at line 3 has been removed
One point section Import3d_Section[1] ending at line 2 has been removed
# 2
# /
# 0 - 1
# \
# 3
1 1 0 0 0 10 -1
2 1 0 0 10 10 1
3 1 0 -5 20 10 2
4 1 0 5 20 10 2
Generates a soma with length=10 and diam=20 - BUT the following warnings are generated:
One point section Import3d_Section[2] ending at line 4 has been removed
One point section Import3d_Section[1] ending at line 3 has been removed
1 1 0 0 -5 2 -1
2 1 0 0 0 5 1
3 1 0 0 2 6 2
4 1 0 0 6 1 3
5 1 0 0 10 7 4
6 1 0 0 15 2 5
Generates a soma with length=20 and diam=8.1 (((2+5)*5 + (5+6)*2 + (6+1)*4 + (1+7)*4 + (7+2)*5)/20 = 8.1)
1 1 0 0 0 10 -1
2 3 0 200 0 10 1
Generates a soma with length=20 and diam=20 BUT no dendrite - the following warning is printed:
One point section Import3d_Section[1] ending at line 2 has been removed
1 1 0 0 0 10 -1
2 3 0 0 0 5 1
3 3 0 200 0 10 2
Generates a soma with length=20 and diam=20 ; and a dendrite with length=200 and diam=15
1 1 0 0 -10 10 -1
2 1 0 0 0 10 1
3 3 0 200 0 10 2
Generates a soma with length=10 and diam=20 BUT no dendrite - the following warning is printed:
One point section Import3d_Section[1] ending at line 3 has been removed
1 1 0 0 -20 10 -1
2 1 0 0 0 10 1
3 3 0 0 0 10 2
4 3 0 200 0 10 3
Generates a soma with length=20 and diam=20 ; and a dendrite with length=200 and diam=20
This seems to indicate that the dendrite cannot get its proximal point from the soma.
1 1 0 0 -20 10 -1
2 1 0 0 0 10 1
3 3 0 0 80 10 2
4 3 0 0 -80 10 2
Generates a soma with length=20 and diam=20 BUT no dendrite - the following warning are printed:.
One point section Import3d_Section[2] ending at line 4 has been removed
One point section Import3d_Section[1] ending at line 3 has been removed
1 1 0 0 -20 10 -1
2 1 0 0 0 10 1
3 3 0 0 0 10 2
4 3 0 0 80 10 3
5 2 0 0 -80 10 3
Generates a soma with length=20 and diam=20 ; and a dendrite with length=80 and diam=20; and an axon with length=80 and diam=20 - But the following warnings are generated
One point section Import3d_Section[1] ending at line 3 has been removed
and child Import3d_Section[2] reattached
and child Import3d_Section[3] reattached
1 3 0 0 0 1 -1
2 3 0 0 10 1 1
3 1 0 0 20 10 2
Generates a dendrite with length=10 and diam=2 and no soma - the following warning is generated
One point section Import3d_Section[1] ending at line 3 has been removed
1 3 0 0 0 1 -1
2 3 0 0 10 1 1
3 1 0 0 20 10 2
4 1 0 0 22 5 3
Generates a soma with length=2 and diam=15 and a dendrite with length=10 and diam=2
1 3 0 1 2 1 -1
2 3 0 9 2 1 1
3 1 0 0 0 10 2
4 1 0 0 2 10 3
5 1 0 0 4 10 4
6 3 0 1 2 1 5
7 3 0 8 2 1 6
Generates the following, unexpected behavior:
sec : Cell.soma[0]
length: 4.0
parent: Cell.dend[0](0.5)
sec : Cell.dend[0]
length: 8.0
parent: None
sec : Cell.dend[1]
length: 9.23606797749979
parent: Cell.soma[0](1)
1 3 0 0 -5 2 -1
Generates nothing
1 3 0 0 -5 2 -1
2 3 0 0 0 2 1
Generates a dendrite with length=5 and diam=4
1 3 0 0 0 1 -1
2 3 0 0 10 1 1
3 2 0 0 20 10 2
Generates an axon with length=10 and diam=2 - BUT the following warning is produced:
One point section Import3d_Section[1] ending at line 3 has been removed
1 3 0 0 0 1 -1
2 3 0 0 10 1 1
3 2 0 0 20 10 2
4 2 0 0 22 5 3
Generates an axon with length=10 and diam=2 and an axon with length=2 and diam=15
(Issues submitted to NEURON here and here)
1 3 0 0 10 10 -1 # dend
2 3 0 0 20 10 1 # dend
3 2 0 0 21 10 2 # axon
4 2 0 0 30 10 3 # axon
Generates a dendrite with length = 10 and diam = 20; and an axon with length = 9 diam = 20
This suggests that the axon and dendrite are not connected at point (0,0,20)
1 1 0 0 0 1 -1 # soma
2 1 0 0 9 1 1 # soma
3 3 0 0 10 10 2 # dend
4 3 0 0 20 10 3 # dend
5 2 0 0 21 10 4 # axon
6 2 0 0 30 10 5 # axon
Generates a soma with length = 9 and diam = 2; a dendrite with length = 10 and diam = 20; and an axon with length = 10 diam = 20
This suggests that the axon and dendrite are connected at point (0,0,20)
- A soma needs to be defined and it needs to be at the root.
- A soma is represented by a series of n≥1 unbranched, serially listed samples.
- A soma is a single cylinder with diameter equal to the piecewise average diameter.
- A single-sample soma (tag 1) at the root will produce a cylinder with length=diameter.
- If a non-soma sample (tag > 1) is to have a soma sample (tag 1) as its parent, it must have the most distal sample of the soma segment as the parent. (This is subject to change depending on the outcome of the NEURON issues.)
- Every non-soma sample (tag > 1) that has a soma sample (tag 1) as its parent, attaches to the created soma cylinder at its midpoint (via a zero-resistance wire).
- If a non-soma sample (tag > 1) has a soma sample (tag 1) as its parent, no segment is created between the sample and its parent, instead that sample is the proximal point of a new segment.
- To create a segment with a certain tag, that is to be attached to the soma, we need at least 2 samples with that tag.