-
Notifications
You must be signed in to change notification settings - Fork 61
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 an unbranched series of n≥1 contiguously numbered 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.
- Every non-soma sample (tag > 1) that has a soma sample as its parent, attaches to the created soma cylinder at its midpoint (via a zero-resistance wire).
- To create a segment with a certain tag, we need at least 2 samples with that tag. The only exception to this is single-sample somas.
- If a sample with (tag > 1) has parent with (tag 1), no segment is created between the sample and its parent, instead that sample is the proximal point of a new segment.