Dear V3aaD developers,

I've already been playing around with the Vaa3D software for few weeks and I really like it. I think it's very user-friendly and powerful. This is the first software I use for reconstructing neurons and I had many questions, most of them are already answered in the instructions and forums. However, there is an issue related to the SWC file that I still don't understand. 

I tried several ways for reconstructing neurons ('right-stroke to define 3D curve', 'trace from one landmark to all others',...) and the one I prefer consists in pinpointing markers in the 3D view and trace paths between 2 markers. A very simple example of that for an axon that bifurcates into two branches would be:

1) Pinpoint marker 1 where the axon starts
2) Pinpoint marker 2 in the bifuraction
3) Pinpoint marker 3 in the Terminal of branch A
4) Pinpoint marker 4 in the Terminal of branch B
5) Trace path between marker 1 and 2, trace path between maker 2 and 3 and finally trace path between marker 2 and 4.

In this way I get reconstructions that resemble the most the raw data from my axons.

However, I realized that the SWC files resulting from my reconstructions look weird (see SWC file 1 at the end of the message) when I compare them to SWC files from your test data, SWC files from Neuromorpho, or even SWC files I get if I reconstruct the very same axonal region by other means, like' right-stroke 3D curve' or 'trace from one landmark to all others' (see SWC file 2 at the end of the message).

Basically, I realized there are problems in the 'parent' column. I guess that this is very relevant for later morphometric analysis of the reconstructions. For example, when I input these SWC files in L-measure software it gives me the following error: the file is found to have some missing compartments. I guess you can tell me why this is happening and how to solve it? May be the way I am tracing the neurons is not the most appropriate one?

Many thanks in advance,

Jesús.

********

SWC File 1 (acquired by: sequentially tracing between 2 markers)

#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

------

SWC File 2 (acquired by trace from 1 landmark to all others):

#name v3d_traced_neuron
#comment 
##n,type,x,y,z,radius,parent
1 3 674.352 710.519 38.747 3.000 -1
2 3 671.968 710.116 38.223 3.625 1
3 3 669.966 711.935 38.171 3.875 2
4 3 667.935 713.920 38.179 4.125 3
5 3 665.904 715.883 38.222 4.375 4
6 3 663.870 717.826 38.226 4.562 5
7 3 661.572 719.510 38.226 4.688 6
8 3 658.482 720.597 38.156 4.750 7
9 3 656.473 722.578 38.190 4.750 8
10 3 655.438 725.337 38.175 4.750 9
11 3 652.385 726.457 38.235 4.750 10
12 3 649.741 727.715 38.190 4.688 11
13 3 646.339 728.113 38.631 4.688 12
14 3 643.727 728.078 39.345 4.750 13
15 3 640.343 728.585 39.760 4.812 14
16 3 638.020 730.110 39.819 4.938 15
17 3 636.059 732.082 40.042 4.812 16
18 3 633.697 733.617 40.131 4.562 17
19 3 630.336 734.447 40.172 4.375 18
20 3 627.991 735.970 40.233 4.250 19
21 3 625.683 737.513 40.355 4.375 20
22 3 622.352 738.437 40.421 4.562 21
23 3 619.768 739.743 40.337 4.625 22
24 3 616.326 740.115 40.737 4.688 23
25 3 614.097 740.724 41.535 4.812 24
26 3 608.000 742.000 42.000 6.000 25
27 3 608.000 742.000 42.000 6.000 -1
28 3 607.946 743.685 41.673 6.000 27
29 3 607.660 743.552 41.239 6.000 28
30 3 608.000 742.000 42.000 6.000 -1
31 3 603.845 742.131 42.018 5.438 30
32 3 603.845 742.131 42.018 5.438 -1
33 3 600.017 741.901 42.144 5.438 32
34 3 596.299 741.382 42.257 5.375 33
35 3 593.756 740.301 42.387 5.250 34
36 3 590.011 739.964 42.362 4.875 35
37 3 586.187 739.822 42.349 4.562 36
38 3 583.957 738.050 42.376 4.312 37
39 3 581.994 736.008 42.326 3.938 38
40 3 579.987 734.014 42.201 3.875 39
41 3 578.008 731.993 42.334 4.000 40
42 3 575.980 730.024 42.217 4.188 41
43 3 574.243 727.764 42.264 4.500 42
44 3 573.380 724.448 42.218 4.688 43
45 3 571.826 722.093 42.181 4.750 44
46 3 570.347 719.715 42.113 4.688 45
47 3 569.381 716.399 42.149 4.625 46
48 3 567.878 714.109 42.121 4.500 47
49 3 567.306 712.084 42.073 4.000 48
50 3 603.845 742.131 42.018 5.438 -1
51 3 606.000 742.000 42.000 5.000 50
52 3 605.913 744.014 41.914 4.312 51
53 3 604.301 746.210 41.957 3.438 52
54 3 604.147 750.027 41.900 2.438 53
55 3 603.794 753.778 41.923 1.688 54
56 3 602.131 756.211 41.662 1.188 55
57 3 602.102 759.985 42.006 1.000 56
58 3 602.103 764.014 41.824 1.125 57
59 3 601.846 767.999 42.043 1.438 58
60 3 601.548 771.724 41.938 1.938 59
61 3 600.312 774.279 41.843 2.562 60
62 3 599.633 777.737 41.872 3.062 61
63 3 598.033 780.054 41.867 3.188 62
64 3 596.680 782.134 42.227 2.938 63
65 3 596.155 784.339 43.176 2.438 64
66 3 595.729 787.744 43.903 1.812 65
67 3 594.290 790.238 43.936 1.438 66
68 3 593.924 793.966 43.999 1.438 67
69 3 593.977 798.025 44.134 1.750 68
70 3 594.461 801.734 44.400 2.375 69
71 3 595.896 804.078 44.584 3.062 70
72 3 596.620 807.605 44.974 4.000 71