Segmentation violation error in swc

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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alexandrapierri
Posts: 69
Joined: Wed Jun 17, 2015 5:31 pm

Segmentation violation error in swc

Post by alexandrapierri »

Hello

I load this morphology with "new Import3d_SWC_read()" and when I plot the voltage, I get a segmentation violation error.
I have used similar morphologies and others worked well. Unsure what I should be looking for that would be causing this error.
Is it a discontinuity in the SWC points? My experimental collaborators have traced this morphology using Fiji.

Only a section of the morphology is loaded.

Code: Select all

# Exported from SNT v4.1.5 on 2023-03-17T13:24:35.394
# https://imagej.net/SNT
#
# All positions and radii in µm
# Voxel separation (x,y,z): 0.621, 0.621, 2.0
#
1	4	317.675997 193.268998 73.555556 0.000000	-1
2	3	322.712996 185.471998 70.666667 0.000000	1
3	3	322.712996 185.471998 70.666667 0.000000	2
4	3	325.403996 181.952998 70.000000 0.000000	3
5	3	324.782996 181.331998 70.000000 0.000000	4
6	3	324.161996 180.710998 70.000000 0.000000	5
7	3	324.161996 180.089998 70.000000 0.000000	6
8	3	324.161996 179.468998 70.000000 0.000000	7
9	3	323.540996 178.847998 68.000000 0.000000	8
10	3	323.540996 178.226998 68.000000 0.000000	9
11	3	323.540996 177.605998 68.000000 0.000000	10
12	3	322.919996 176.984998 68.000000 0.000000	11
13	3	322.919996 176.363998 68.000000 0.000000	12
14	3	322.919996 175.742998 68.000000 0.000000	13
15	3	322.919996 175.121998 68.000000 0.000000	14
16	3	322.919996 174.500998 68.000000 0.000000	15
17	3	322.919996 173.879998 68.000000 0.000000	16
18	3	322.298996 173.258998 68.000000 0.000000	17
19	3	321.677996 172.637998 68.000000 0.000000	18
20	3	321.056996 172.016998 68.000000 0.000000	19
21	3	320.435996 171.395998 68.000000 0.000000	20
22	3	319.814996 170.774998 68.000000 0.000000	21
23	3	319.193996 170.153998 68.000000 0.000000	22
24	3	318.572996 169.532998 68.000000 0.000000	23
25	3	317.951996 169.532998 68.000000 0.000000	24
26	3	317.330996 168.911998 68.000000 0.000000	25
27	3	316.709996 168.290998 68.000000 0.000000	26
28	3	316.088996 168.290998 68.000000 0.000000	27
29	3	315.467996 167.669998 68.000000 0.000000	28
30	3	314.846996 167.048998 68.000000 0.000000	29
31	3	314.225996 166.427998 68.000000 0.000000	30
32	3	313.604996 166.427998 68.000000 0.000000	31
33	3	312.983996 165.806998 68.000000 0.000000	32
34	3	312.362996 165.185998 68.000000 0.000000	33
35	3	311.741996 164.564998 68.000000 0.000000	34
36	3	311.120996 163.943998 68.000000 0.000000	35
37	3	310.499996 163.943998 68.000000 0.000000	36
38	3	309.878996 163.943998 68.000000 0.000000	37
39	3	309.257996 163.943998 68.000000 0.000000	38
40	3	308.636996 163.943998 68.000000 0.000000	39
41	3	308.015996 163.943998 68.000000 0.000000	40
42	3	307.394996 163.943998 68.000000 0.000000	41
43	3	306.773996 163.322998 68.000000 0.000000	42
44	3	306.152996 162.701998 68.000000 0.000000	43
45	3	305.531996 163.322998 68.000000 0.000000	44
46	3	304.910996 162.701998 68.000000 0.000000	45
47	3	304.289996 162.701998 68.000000 0.000000	46
48	3	303.668996 162.080998 68.000000 0.000000	47
49	3	303.047996 162.080998 68.000000 0.000000	48
50	3	302.426996 162.080998 68.000000 0.000000	49
51	3	301.805996 162.080998 68.000000 0.000000	50
52	3	301.184996 162.080998 68.000000 0.000000	51
53	3	300.563996 162.080998 68.000000 0.000000	52
54	3	299.942996 162.080998 68.000000 0.000000	53
55	3	299.321996 162.080998 68.000000 0.000000	54
56	3	298.700996 161.459998 68.000000 0.000000	55
57	3	298.079996 161.459998 68.000000 0.000000	56
58	3	297.458996 161.459998 70.000000 0.000000	57
59	3	296.837996 161.459998 70.000000 0.000000	58
60	3	296.216996 161.459998 70.000000 0.000000	59
61	3	295.595996 160.838998 70.000000 0.000000	60
62	3	294.974996 160.217998 70.000000 0.000000	61
63	3	294.353996 160.217998 70.000000 0.000000	62
64	3	293.732996 159.596998 70.000000 0.000000	63
65	3	293.111996 159.596998 70.000000 0.000000	64
66	3	292.490996 158.975998 70.000000 0.000000	65
67	3	291.869996 158.975998 70.000000 0.000000	66
68	3	291.248996 158.354998 70.000000 0.000000	67
69	3	290.627996 157.733998 70.000000 0.000000	68
70	3	290.006996 157.733998 70.000000 0.000000	69
71	3	289.385996 157.733998 70.000000 0.000000	70
72	3	288.764996 157.112998 70.000000 0.000000	71
73	3	288.143996 156.491998 70.000000 0.000000	72
74	3	287.522996 155.870998 70.000000 0.000000	73
75	3	286.901996 155.249998 70.000000 0.000000	74
76	3	286.280996 154.628998 72.000000 0.000000	75
77	3	285.659996 154.007998 72.000000 0.000000	76
78	3	285.659996 153.386998 72.000000 0.000000	77
79	3	285.038996 152.765998 72.000000 0.000000	78
80	3	284.417996 152.144998 72.000000 0.000000	79
81	3	283.796996 151.523998 72.000000 0.000000	80
82	3	283.175996 150.902998 72.000000 0.000000	81
83	3	283.175996 150.281998 72.000000 0.000000	82
84	3	282.554996 149.660998 72.000000 0.000000	83
85	3	281.933996 149.039998 72.000000 0.000000	84
86	3	281.933996 148.418998 72.000000 0.000000	85
87	3	281.933996 147.797998 72.000000 0.000000	86
88	3	281.312996 147.176998 70.000000 0.000000	87
89	3	281.933996 147.797998 72.000000 0.000000	88
90	3	281.312996 147.176998 74.000000 0.000000	89
91	3	280.691996 146.555998 76.000000 0.000000	90
92	3	280.070996 145.934998 76.000000 0.000000	91
93	3	279.449996 145.313998 76.000000 0.000000	92
94	3	278.828996 144.692998 76.000000 0.000000	93
95	3	278.828996 144.071998 76.000000 0.000000	94
96	3	278.207996 143.450998 76.000000 0.000000	95
97	3	277.586996 142.829998 78.000000 0.000000	96
98	3	276.965996 142.208998 78.000000 0.000000	97
99	3	276.344996 141.587998 80.000000 0.000000	98
100	3	275.723996 141.587998 80.000000 0.000000	99
101	3	275.102996 141.587998 80.000000 0.000000	100
102	3	274.481996 141.587998 80.000000 0.000000	101
103	3	273.860996 141.587998 80.000000 0.000000	102
104	3	273.239996 141.587998 80.000000 0.000000	103
105	3	272.618996 141.587998 80.000000 0.000000	104
106	3	271.997996 141.587998 80.000000 0.000000	105
107	3	271.376996 142.208998 82.000000 0.000000	106
108	3	270.755996 142.208998 82.000000 0.000000	107
109	3	270.134996 142.208998 82.000000 0.000000	108
110	3	269.513996 142.208998 82.000000 0.000000	109
111	3	268.892996 142.829998 82.000000 0.000000	110
112	3	268.271996 142.829998 82.000000 0.000000	111
113	3	267.650997 142.829998 82.000000 0.000000	112
114	3	267.029997 142.829998 82.000000 0.000000	113
115	3	266.408997 142.829998 82.000000 0.000000	114
116	3	265.787997 142.829998 82.000000 0.000000	115
117	3	265.166997 143.450998 82.000000 0.000000	116
thank you,
Alexandra
ted
Site Admin
Posts: 6317
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Segmentation violation error in swc

Post by ted »

Tell your experimental collaborators the following:

1. There are large (in some cases, huge) discontinuities in the z direction. You can see this yourself--just look at the values in the fifth field of each data line. That alone would make these data not useful for computational modeling.

2. All diameters are zero. Again, you can see this for yourself (the numbers in the 6th field are the diameters). That's another reason why these data are not useful for modeling.

Correction: the numbers in the 6th field are the radii (half of the apparrent width at the location where the measurement was made).
alexandrapierri
Posts: 69
Joined: Wed Jun 17, 2015 5:31 pm

Re: Segmentation violation error in swc

Post by alexandrapierri »

thank you very much for your response Ted

Regarding point 2. indeed I have noticed this myself and had decided to artifially add radius.
Based on the data at my disposal I can estimate average radius per section. I have 4 sections, so four average radius values.
That is not an ideal solution but my understanding is that experimentalists should have traced left and right of the dendrite as they traced along the tree to acount for diameter thickness. Is that correct?

thanks again.
ted
Site Admin
Posts: 6317
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Segmentation violation error in swc

Post by ted »

Do what you like, but if your time and effort are worth anything, think hard before using this anatomical data in your models. Especially since so much morphometric data is available from NeuroMorpho.org that is not affected by these artifacts. And if you use flawed anatomical data, when it comes time to publish results, be prepared to justify your decision to reviewers.
alexandrapierri
Posts: 69
Joined: Wed Jun 17, 2015 5:31 pm

Re: Segmentation violation error in swc

Post by alexandrapierri »

I see, understood.Thank you!
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