Comments (8)
MarcelBeining
commented on May 25, 2024
Hi @naureeng ,
hard to say without having the swc file. And what do you mean with half the dendrites? Do you have region names for your tree? Do you see anything obvious when running dissect_tree with the -s option to see the sectioning?
Why was it necessary to load your swc with the -r option? What was repaired (there should be some info in the console about it)?
Best
Marcel
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naureeng
commented on May 25, 2024
Hello Marcel,
Our file is "FR130_1_tracing.swc" :
https://github.com/naureeng/cameraLucida/tree/master/Example_data/FR130
We do not have region names for the tree. The -s option shows good sectioning. The issue for me is in the output of:
[sect, vec] = dissect_tree(rtree);
sect does not include all the branches. The output appears as:
1 3
3 4
4 8
8 10
10 13
13 19
19 32
32 37
37 51
51 56
51 57
The first 10 pairs are continuous segments and the last pair is 51 connected to 57. When I count segments in this way, half the nodes are missed. Is there an issue with how I am interpreting the output of sect ?
There was no repair, I believe the default to the .swc file format is -r
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MarcelBeining
commented on May 25, 2024
Hm, so when I download your swc file and execute exactly your script I get as sect:
1 1
1 3
3 4
4 8
8 10
10 13
13 19
19 32
32 37
37 51
51 56
51 57
37 68
37 79
32 98
32 108
19 142
13 144
144 148
148 171
148 188
144 200
10 222
8 225
225 226
226 239
239 264
239 279
226 289
225 298
298 312
298 324
225 339
4 341
341 342
342 344
344 346
346 360
360 394
360 398
398 411
398 423
398 426
346 443
344 479
342 488
488 506
506 507
507 524
507 535
506 541
488 556
341 563
563 574
574 576
563 583
1 587
587 592
592 597
597 598
598 611
598 623
592 625
625 640
625 650
587 651
651 656
656 657
657 672
657 683
651 688
688 703
688 711
587 714
714 716
716 726
726 734
716 743
743 747
714 763
1 767
767 769
769 770
770 775
775 791
775 801
770 809
769 815
815 829
829 832
829 834
815 841
769 864
767 867
867 870
870 885
870 897
867 917
1 966
1 969
969 970
970 971
971 987
971 1000
970 1018
969 1019
1019 1022
1022 1033
1022 1043
1019 1060
1 1063
1063 1066
1066 1068
1068 1086
1068 1098
1066 1108
1063 1121
1121 1124
1121 1125
1 1127
1127 1130
1130 1131
1131 1133
1133 1146
1133 1152
1131 1165
1127 1183
What treestoolbox version are you using?
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naureeng
commented on May 25, 2024
Hello Marcel,
I get the same output as you. I downloaded the most recent one from github and the help line is:
'the TREES toolbox Copyright (C) 2009 - 2018 Hermann Cuntz
The issue is maybe in how I interpreting the sect output. I label each of those start:end pairs in sect as continuous or a 1-point connection. When I do this, half the points are not classified.
sect_corr = sect;
sect_classify = ones(length(sect_corr),1);
for i = 2:length(sect_corr)
if sect_corr(i,1) == sect_corr(i-1,2)
sect_classify(i) = 1;
else
sect_classify(i) = 2;
end
end
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MarcelBeining
commented on May 25, 2024
When I run your code, All sect_classify values have a 1 or a 2, so all the 127 sections that sect comprises have a class now. I don't get what you're missing :-)
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naureeng
commented on May 25, 2024
Hello Marcel,
Apologies for my late reply and not being clear! Using sect_classify, I build a list of nodes where each row is a branch. With the values of sect there are points that are not included in either the continuous (1) or 1-point segments (2). These are those points:
- `58
- 59
- 60
- 61
- 62
- 63
- 64
- 65
- 66
- 67
- 69
- 70
- 71
- 72
- 73
- 74
- 75
- 76
- 77
- 78
- 80
- 81
- 82
- 83
- 84
- 85
- 86
- 87
- 88
- 89
- 90
- 91
- 92
- 93
- 94
- 95
- 96
- 97
- 99
- 100
- 101
- 102
- 103
- 104
- 105
- 106
- 107
- 109
- 110
- 111
- 112
- 113
- 114
- 115
- 116
- 117
- 118
- 119
- 120
- 121
- 122
- 123
- 124
- 125
- 126
- 127
- 128
- 129
- 130
- 131
- 132
- 133
- 134
- 135
- 136
- 137
- 138
- 139
- 140
- 141
- 143
- 172
- 173
- 174
- 175
- 176
- 177
- 178
- 179
- 180
- 181
- 182
- 183
- 184
- 185
- 186
- 187
- 189
- 190
- 191
- 192
- 193
- 194
- 195
- 196
- 197
- 198
- 199
- 201
- 202
- 203
- 204
- 205
- 206
- 207
- 208
- 209
- 210
- 211
- 212
- 213
- 214
- 215
- 216
- 217
- 218
- 219
- 220
- 221
- 223
- 224
- 265
- 266
- 267
- 268
- 269
- 270
- 271
- 272
- 273
- 274
- 275
- 276
- 277
- 278
- 280
- 281
- 282
- 283
- 284
- 285
- 286
- 287
- 288
- 290
- 291
- 292
- 293
- 294
- 295
- 296
- 297
- 313
- 314
- 315
- 316
- 317
- 318
- 319
- 320
- 321
- 322
- 323
- 325
- 326
- 327
- 328
- 329
- 330
- 331
- 332
- 333
- 334
- 335
- 336
- 337
- 338
- 340
- 395
- 396
- 397
- 412
- 413
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- 415
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- 422
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- 425
- 427
- 428
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- 555
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- 559
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- 562
- 577
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- 582
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- 612
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- 621
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- 641
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- 646
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- 649
- 673
- 674
- 675
- 676
- 677
- 678
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- 681
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- 684
- 685
- 686
- 687
- 704
- 705
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- 708
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- 710
- 712
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- 735
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- 748
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- 998
- 999
- 1001
- 1002
- 1003
- 1004
- 1005
- 1006
- 1007
- 1008
- 1009
- 1010
- 1011
- 1012
- 1013
- 1014
- 1015
- 1016
- 1017
- 1034
- 1035
- 1036
- 1037
- 1038
- 1039
- 1040
- 1041
- 1042
- 1044
- 1045
- 1046
- 1047
- 1048
- 1049
- 1050
- 1051
- 1052
- 1053
- 1054
- 1055
- 1056
- 1057
- 1058
- 1059
- 1061
- 1062
- 1087
- 1088
- 1089
- 1090
- 1091
- 1092
- 1093
- 1094
- 1095
- 1096
- 1097
- 1099
- 1100
- 1101
- 1102
- 1103
- 1104
- 1105
- 1106
- 1107
- 1109
- 1110
- 1111
- 1112
- 1113
- 1114
- 1115
- 1116
- 1117
- 1118
- 1119
- 1120
- 1126
- 1147
- 1148
- 1149
- 1150
- 1151
- 1153
- 1154
- 1155
- 1156
- 1157
- 1158
- 1159
- 1160
- 1161
- 1162
- 1163
- 1164
- 1166
- 1167
- 1168
- 1169
- 1170
- 1171
- 1172
- 1173
- 1174
- 1175
- 1176
- 1177
- 1178
- 1179
- 1180
- 1181
- 1182`
I found a way to use the adjacency matrix to fix this, so I can close this issue after your reply. Hope what I wrote was clear, many thanks for your time!
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MarcelBeining
commented on May 25, 2024
Hi @naureeng ,
I guess what you tried to do with sect from dissect_tree is something like
for n=1:length(sect)
branchNodes{n} = sect (n,1):sec(n,2);
end
right?
This is not possible as the node IDs are not necessarily in order from branch start to branch end!
Have you looked into par_tree? This gives you a matrix of adjacent node IDs back to the root for each node. You can use it with the information from sect to find all IDs between sect(n,2) back to sect(n,1) .
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naureeng
commented on May 25, 2024
Yes, exactly! I did not look at par_tree but I used the adjacency matrix to identify segments. I'll take a look, thank you for your help and time!
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