Vaa3d swc files

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oren
Posts: 54
Joined: Fri Mar 22, 2013 1:03 am

Vaa3d swc files

Post by oren » Sat Apr 06, 2013 4:11 pm

As anyone ever had an experience with swc files created from the Vaa3d software?
I have some swc files created from that software but I can not read them with Neuron Import3D. I also have not found any converter.
The only software that I found that is able to read this files is NeuroMantic. ( But it also have problems with long swc files)

This is a example from one of the swc file

Code: Select all

#name v3d_traced_neuron
#comment 
##n,type,x,y,z,radius,parent
1 3 607.660 743.552 41.239 6.000 2
2 3 607.997 743.459 41.810 5.500 3
3 3 610.231 742.390 41.851 5.188 4
4 3 613.704 741.602 41.789 5.000 5
5 3 616.073 740.534 41.482 5.000 6
6 3 618.284 740.023 40.649 5.000 7
7 3 621.685 739.474 40.405 5.000 8
8 3 624.018 737.973 40.391 4.875 9
9 3 626.296 736.341 40.274 4.625 10
10 3 629.718 735.656 40.166 4.500 11
11 3 632.105 734.155 40.197 4.438 12
12 3 634.153 732.312 40.084 4.375 13
13 3 636.476 730.768 39.994 4.438 14
14 3 639.719 729.662 39.798 4.438 15
15 3 642.046 728.466 39.418 4.500 16
16 3 644.299 728.081 38.604 4.688 17
17 3 647.769 727.778 38.234 4.812 18
18 3 650.433 726.622 38.273 4.938 19
19 3 653.741 725.688 38.238 5.000 20
20 3 656.018 724.001 38.221 5.000 21
21 3 658.023 722.030 38.194 4.938 22
22 3 660.033 720.038 38.182 4.750 23
23 3 662.049 718.060 38.186 4.500 24
24 3 664.053 716.067 38.152 4.125 25
25 3 666.163 714.221 38.144 3.750 26
26 3 668.142 712.242 38.111 3.500 27
27 3 670.328 710.502 38.193 3.250 28
28 3 674.352 710.519 38.747 3.000 -1
29 3 567.306 712.084 42.073 4.000 30
30 3 567.633 712.435 42.133 4.312 31
31 3 568.323 715.684 42.099 4.500 32
32 3 569.854 718.078 42.098 4.625 33
33 3 571.522 720.368 42.112 4.688 34
34 3 572.286 723.740 42.181 4.812 35
35 3 573.772 726.154 42.247 4.812 36
36 3 575.712 728.192 42.309 4.688 37
37 3 577.866 730.086 42.276 4.562 38
38 3 579.612 732.359 42.286 4.375 39
39 3 580.375 735.615 42.185 4.312 40
40 3 582.040 737.919 42.237 4.500 41
41 3 584.321 739.551 42.371 4.750 42
42 3 587.943 740.106 42.358 5.000 43
43 3 592.046 739.914 42.360 5.188 44
44 3 595.735 740.428 42.325 5.250 45
45 3 598.275 741.533 42.192 5.250 46
46 3 601.999 742.012 42.039 5.312 47
47 3 605.808 742.384 41.973 5.438 48
48 3 607.927 743.425 41.804 5.625 49
49 3 607.660 743.552 41.239 6.000 -1
50 3 596.620 807.605 44.974 4.000 51
51 3 595.973 805.908 44.641 3.938 52
52 3 594.484 803.757 44.439 3.562 53
53 3 593.913 800.024 44.183 3.000 54
54 3 593.803 795.964 44.037 2.500 55
55 3 594.224 792.235 43.869 2.062 56
56 3 595.799 789.734 44.172 1.812 57
57 3 596.045 786.288 43.517 1.875 58
58 3 596.148 783.781 42.278 2.125 59
59 3 596.560 780.344 41.887 2.250 60
60 3 598.333 778.118 41.857 2.312 61
61 3 599.710 775.762 41.854 2.125 62
62 3 600.385 772.293 41.897 1.688 63
63 3 601.666 769.750 41.992 1.375 64
64 3 601.991 766.025 41.862 1.125 65
65 3 602.101 762.013 41.981 1.000 66
66 3 602.046 757.980 41.914 1.125 67
67 3 602.181 754.217 41.897 1.500 68
68 3 603.733 751.764 42.021 2.188 69
69 3 604.016 747.985 41.929 3.188 70
70 3 604.502 744.415 41.996 4.250 71
71 3 607.527 743.883 41.842 5.125 72
72 3 607.660 743.552 41.239 6.000 -1
also as you can see its x y z points are pixel points and need to be corrected via the voxel diameters.


Thank You.

ted
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Re: Vaa3d swc files

Post by ted » Sun Apr 07, 2013 3:35 pm

The data file appears to violate the swc file format. In every swc file that I have ever seen, the "parent index" (last number on each line, which specifies which data point is the parent of the current point) is always less than the "point index" (first number on each line). Not the case with your example.

The file happens to contain multiple root nodes (points that have no parent, i.e. parent index is -1), which suggests that it contains data from more than one cell, or more likely that it contains orphan branches i.e. branches that, by mistake, have no parent branch.

oren
Posts: 54
Joined: Fri Mar 22, 2013 1:03 am

Re: Vaa3d swc files

Post by oren » Mon Apr 08, 2013 9:25 am

Thank You.
I've build matlab script's that split all the -1 roots apart and build them in the correct swc specification.
If anyone ever need help I can send them to him.

Plus there is a plugin in the Vaa3d software that is called sort_neuron.. It suppose to convert the swc file to the right specification (It does work with some swc files, But not with all).

Chiara
Posts: 1
Joined: Thu Dec 25, 2014 6:04 pm

Re: Vaa3d swc files

Post by Chiara » Sun Dec 28, 2014 2:32 pm

Hello,

I am having exactly the same problem with the swc files from Vaa3d!!

I am trying to use the sort_neuron plugin of Vaa3d but I am having some problems to compile it. If you wrote a matlab script that adjusts these swc files, I would greatly appreciate if you could send it to me... it would save me lots of time!

Thank you very much!

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