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. Author manuscript; available in PMC: 2021 Feb 1.
Published in final edited form as: J Neurosci Methods. 2019 Nov 21;331:108529. doi: 10.1016/j.jneumeth.2019.108529

Table 2. Example 3D neuronal Sholl output.

Classification of a dendrite as primary, intermediate, or terminal, independent of user tracing, is not currently supported in ImageJ. Analyses were performed on a test 3D image (not shown). (V1x, V1y, V1z) and (V2x, V2y, V2z) are the (x, y, z) position of the starting and ending voxel of each branch, respectively. Branch length and thickness are in microns. Branch (Dendrite) Type: TER – terminal, INT – intermediate, PRI – primary.

Skeleton ID Branch Length V1x V1y V1z V2x V2y V2z Branch Type Euclidean Distance Running Avg. Length Max Thickness Avg. Thickness Avg. Intensity
1 1 14.41344 214.08 261.44 28 225.28 255.04 11 INT 21.3401 13.0496 0.90496 0.58016 255
2 1 9.32544 202.56 271.04 35 209.92 267.2 30 INT 9.690986 8.14912 1.15392 0.64672 255
3 1 9.21568 189.44 283.2 13 195.2 277.12 32 INT 20.76401 8.35104 1.01184 0.6368 255
4 1 8.7632 167.04 302.4 66 173.44 297.6 78 TER 14.42221 8.21696 1.15392 0.62528 255
5 1 8.63072 183.68 288.32 27 189.44 283.2 31 INT 8.682857 6.5152 1.43104 0.88224 255
6 1 7.85792 231.36 250.56 2 236.8 246.08 32 INT 30.81662 6.50496 0.90496 0.49824 255
7 1 7.8032 178.88 293.12 8 183.68 288.32 31 INT 23.98083 6.81152 1.35776 0.88416 255
8 1 7.67072 209.92 267.2 21 214.08 261.44 21 INT 7.105153 5.98944 0.71552 0.50752 255
9 1 7.27296 281.6 214.4 36 287.68 211.52 36 PRI 6.727615 5.76128 0.64 0.41536 255
10 1 6.95296 197.44 274.56 46 202.56 271.04 37 PRI 10.9364 5.5104 1.01184 0.6528 255
11 1 6.5552 273.92 216.96 45 279.68 215.04 47 PRI 6.392496 5.6672 0.71552 0.47936 255
12 1 5.80544 174.72 296.64 3 178.88 293.12 9 INT 8.105307 5.05984 0.96 0.45472 255
13 1 5.78272 260.16 223.68 20 264.96 221.76 2 INT 18.72769 3.84768 0.64 0.41056 255
14 1 5.2752 255.68 226.24 38 259.2 223.36 46 PRI 9.202434 4.32896 0.64 0.44416 255
15 1 5.19456 243.52 235.84 44 247.36 233.92 47 PRI 5.237557 3.62752 0.64 0.50848 255
16 1 5.08768 225.28 255.04 40 228.8 252.16 48 PRI 9.202434 3.96832 0.96 0.68384 255
17 1 4.76768 228.8 252.16 44 230.08 249.28 36 PRI 8.598418 3.29312 0.96 0.55904 255
18 1 4.50272 266.24 220.8 38 269.76 218.88 49 PRI 11.70798 3.78944 0.64 0.4864 255
19 1 3.9952 240 241.28 40 242.56 238.72 41 PRI 3.755955 3.10688 0.64 0.51424 255
20 1 3.9952 242.56 238.72 1 243.52 235.84 25 INT 24.19124 3.03104 0.64 0.55328 255
21 1 3.6752 195.2 277.12 15 197.44 274.56 18 INT 4.535548 2.82944 0.96 0.56256 255
22 1 3.6752 251.84 229.44 1 254.4 227.2 11 INT 10.56273 2.76704 0.71552 0.6736 255
23 1 3.28384 236.8 246.08 15 238.72 243.52 24 INT 9.551963 1.35776 0.64 0.4176 255
24 1 2.95776 247.36 233.92 17 248 231.68 1 INT 16.16871 2.25632 0.64 0.4224 255
25 1 2.95776 270.72 219.2 34 273.28 218.24 9 INT 25.14906 1.6336 0.90496 0.5296 255
26 1 2.50496 292.48 209.28 73 290.24 209.92 64 TER 9.296623 2.2992 0.64 0.38464 255
27 1 2.45024 236.8 246.08 44 236.8 246.08 43 PRI 1 1.35776 0.45248 0.40832 255
28 1 2.39328 230.08 249.28 46 231.36 250.56 38 PRI 8.202244 1.35776 0.71552 0.45216 255
29 1 2.31776 260.48 221.76 52 260.16 223.68 72 TER 20.0945 2.19488 0.64 0.41056 255
30 1 2.26048 228.8 252.16 6 230.4 250.88 30 INT 24.08731 0.99776 0.96 0.69216 255
31 1 2.18496 241.6 243.52 72 239.68 242.88 58 TER 14.14553 2.0096 0.45248 0.34208 255
32 1 2.18496 279.68 215.04 28 281.6 214.4 32 INT 4.482856 1.01504 0.71552 0.45216 255
33 1 2.10432 183.68 286.4 71 183.68 288.32 65 TER 6.299714 2.15968 0.96 0.54624 255
34 1 1.99776 239.68 242.88 21 240 241.28 18 INT 3.415026 1.26272 0.64 0.46624 255
35 1 1.99776 250.24 230.4 20 251.84 229.44 33 INT 13.13323 1.42016 0.64 0.54624 255
36 1 1.86496 173.44 297.6 3 174.72 296.64 6 INT 3.4 0.97952 1.31936 1.07072 255
37 1 1.86496 254.4 227.2 34 255.68 226.24 19 INT 15.08509 0.99776 0.71552 0.57888 255
38 1 1.73248 211.52 266.88 66 209.92 267.2 46 TER 20.06645 1.78752 0.45248 0.38624 255
39 1 1.73248 288.96 210.56 11 290.24 209.92 8 INT 3.323853 1.29728 0.64 0.576 255
40 1 1.67776 264.96 221.76 7 266.24 220.8 29 INT 22.05811 0.90496 0.71552 0.6176 255
41 1 1.67776 249.28 231.68 33 250.24 230.4 35 INT 2.56125 0.45248 0.71552 0.65888 255
42 1 1.67552 230.08 249.28 31 230.4 250.88 20 INT 11.12036 0.64 0.71552 0.45216 255
44 1 1.54496 230.4 250.88 29 231.36 250.56 26 INT 3.16607 0.77248 0.45248 0.36416 255
45 1 1.54496 273.28 218.24 28 273.92 216.96 23 INT 5.200769 0.99776 0.90496 0.54624 255
46 1 1.488 232.64 251.2 74 231.36 250.56 73 TER 1.745852 1.39328 0.32 0.32 255
47 1 1.41248 260.48 224.96 60 260.16 223.68 66 TER 6.143354 1.41248 0.64 0.43328 255
48 1 1.35776 237.76 242.56 61 238.72 243.52 51 TER 10.09174 1.35776 0.64 0.43328 255
49 1 1.35776 264 220.8 57 264.96 221.76 44 TER 13.0707 1.35776 0.64 0.4 255
50 1 1.35776 279.36 214.08 59 279.68 215.04 65 TER 6.084735 1.35776 0.71552 0.45184 255
51 1 1.35552 229.12 250.88 77 228.8 252.16 56 TER 21.04141 1.35552 0.96 0.53344 255
52 1 1.28 248 231.68 2 249.28 231.68 26 INT 24.03411 0.32 0.64 0.47072 255
53 1 1.22496 196.16 277.76 43 195.2 277.12 45 TER 2.308939 1.22496 0.96 0.70944 255
54 1 1.22496 243.52 239.36 61 242.56 238.72 81 TER 20.03325 1.22496 0.64 0.42656 255
55 1 1.22496 238.72 243.52 18 239.68 242.88 5 INT 13.0511 0.90496 0.71552 0.61216 255
56 1 1.22496 172.48 296.96 62 173.44 297.6 50 TER 12.05534 1.0624 0.96 0.57888 255
57 1 1.22496 175.68 297.28 73 174.72 296.64 50 TER 23.02892 1.13024 0.96 0.53344 255
58 1 1.22496 182.72 287.68 70 183.68 288.32 76 TER 6.109926 1.0624 0.96 0.56 255
59 1 1.22496 188.8 282.24 61 189.44 283.2 46 TER 15.04431 1.0624 1.01184 0.57312 255
60 1 1.22496 203.2 272 57 202.56 271.04 81 TER 24.02772 1.0624 1.01184 0.75232 255
61 1 1.22496 252.48 230.4 65 251.84 229.44 69 TER 4.163076 1.13024 0.64 0.42656 255
62 1 1.22496 272.96 216.32 81 273.92 216.96 63 TER 18.03694 1.0624 0.32 0.32 255
63 1 1.168 288.64 212.16 74 287.68 211.52 49 TER 25.02661 1.168 0.32 0.32 255
64 1 1.09248 179.84 293.44 82 178.88 293.12 74 TER 8.063746 0.99776 0.45248 0.36416 255
65 1 1.09248 225.92 255.68 53 225.28 255.04 48 TER 5.08126 0.99776 0.90496 0.60352 255
66 1 1.09248 288.64 209.6 65 288.96 210.56 46 TER 19.02693 0.97728 0.64 0.4 255
67 1 1.09248 249.28 231.68 23 249.28 231.68 18 INT 5 0.77248 0.64 0.53344 255
68 1 1.09248 259.2 223.36 21 260.16 223.68 20 INT 1.422674 0.32 0.64 0.5776 255
69 1 1.09248 269.76 218.88 10 270.72 219.2 22 INT 12.04259 0.32 0.64 0.64 255
70 1 0.90496 265.6 220.16 47 266.24 220.8 67 TER 20.02047 0.90496 0.64 0.47072 255
71 1 0.90496 287.04 210.88 59 287.68 211.52 46 TER 13.03147 0.90496 0.32 0.32 255
72 1 0.77248 197.12 273.92 81 197.44 274.56 48 TER 33.00776 0.67776 0.64 0.42656 255
73 1 0.77248 213.76 260.8 49 214.08 261.44 84 TER 35.00731 0.67776 0.64 0.42656 255
74 1 0.77248 230.4 248.64 43 230.08 249.28 74 TER 31.00826 0.81024 0.71552 0.496 255
75 1 0.77248 249.92 229.76 49 250.24 230.4 66 TER 17.01505 0.67776 0.64 0.42656 255
76 1 0.77248 269.44 218.24 45 269.76 218.88 44 TER 1.229634 0.67776 0.64 0.42656 255
77 1 0.77248 271.04 219.84 68 270.72 219.2 69 TER 1.229634 0.77248 0.64 0.48 255
78 1 0.77248 273.6 218.88 65 273.28 218.24 49 TER 16.01599 0.67776 0.90496 0.72832 255
79 1 0.77248 281.92 215.04 44 281.6 214.4 81 TER 37.00692 0.77248 0.45248 0.38624 255
80 1 0.64 239.36 241.28 78 240 241.28 60 TER 18.01137 0.64 0.45248 0.36416 255
81 1 0.45248 255.36 225.92 71 255.68 226.24 70 TER 1.097634 0.45248 0.32 0.32 255
82 1 0.45248 258.88 223.04 73 259.2 223.36 56 TER 17.00602 0.45248 0.45248 0.38624 255
83 1 0.45248 289.92 209.6 78 290.24 209.92 72 TER 6.017042 0.45248 0.32 0.32 255
84 1 0.32 243.2 235.84 83 243.52 235.84 58 TER 25.00205 0.32 0.64 0.48 255
85 1 0.32 247.68 231.68 74 248 231.68 50 TER 24.00213 0.32 0.32 0.32 255