Introduction
Methods
Single neuron labeling
Recovery and reconstruction of morphologies
Quantification of morphological properties
Measure # | Name | Description |
---|---|---|
1 | Number of stems | Number of primary dendrites |
2 | Stem diameter—mean | Average diameter of dendrite stems (µm) |
3 | Stem diameter—sum | Sum of the diameter of all dendrite stems (µm) |
4 | Stem diameter—maximum | Maximal diameter of dendrite stems (µm) |
5 | Stem directionality | Directionality of dendrite stems; for definition see “Methods” |
6 | Dendrites—total length | The summed length of all of a neuron’s dendrites (µm) |
7 | Dendrite diameter—mean | Average diameter of the dendrites (µm) |
8 | Dendrites—longest single path length | Longest soma-to-tip dendrite path length (µm) |
9 | Number of bifurcations | Number of bifurcation points on the dendritic tree |
10 | Local bifurcation angle—mean | Angle formed at the vertex of a bifurcation, averaged over all bifurcations |
11 | Remote bifurcation angle—mean | Angle to the tips of two daughter branches of a bifurcation, averaged over all bifurcations |
12 | Number of branches | Number of segments (between two branch points or between a branch point and a tip) |
13 | Branch order—maximum | The number of branches coming off the most-branching dendrite on the tree |
14 | Number of tips | Number of dendrite terminal points within the imaged slice |
15 | Number of cut tips | Number of dendrites running out of the imaged slice |
16 | Number of tips—total | Total number of dendrite terminal points on the reconstructed morphology |
17 | Soma area | Area of the 2D projection of the soma |
18 | Hull volume | Volume of the convex hull containing all of the neuron’s dendrites (µm3) |
19 | Soma-to-hull distance | Smallest distance between the soma and the hull containing all of the neuron’s dendrites (µm) |
20 | Soma-to-center of gravity distance | Distance between the soma and the average of all points of the reconstructed morphology (µm) |
21 | Reach—maximum | Furthest reach of the dendritic tree away from the soma (µm) |
22 | Straightness | Maximal reach divided by maximal path length |
23 | Mean contraction | Furthest reach divided by longest path length of each tree arising from the primary dendrites, averaged over the number of primary dendrites |
24 | Hausdorff dimension | Measure of fractal dimension (Mizrahi et al. 2000) |
25 | Mean fragmentation | Number of compartments that form a branch between two bifurcation points, or between a bifurcation and a terminal tip |
Statistical analyses
Reconstruction and analysis of IO soma distribution
Results
Variability of IO dendritic morphology
Quantitative analyses reveal a continuum in neuronal morphology
Measure names | Welch’s ANOVA | Levene’s test for equality of variance |
---|---|---|
Number of stems | < 0.0001 | 0.2562 |
Stem diameter—mean |
0.0129
| 0.7094 |
Stem diameter—sum | < 0.0001 |
0.0071
|
Stem diameter—maximum |
0.0004
| 0.4644 |
Stem directionality | 0.5522 | 0.8356 |
Dendrites—total length | < 0.0001 | 0.0743 |
Dendrite diameter—mean |
0.0005
| 0.6540 |
Dendrites—longest single path length | < 0.0001 | 0.3177 |
Number of bifurcations | < 0.0001 | < 0.0001 |
Local bifurcation angle—mean | 0.2153 | 0.1322 |
Remote bifurcation angle—mean | 0.7173 | 0.1410 |
Number of branches | < 0.0001 | < 0.0001 |
Branch order—maximum |
0.0002
|
0.0295
|
Number of tips |
0.0065
|
0.0460
|
Number of cut tips |
0.0006
| 0.1199 |
Number of tips—total | < 0.0001 |
0.0332
|
Soma area | < 0.0001 |
0.0279
|
Hull volume |
0.0152
| 0.3412 |
Soma-to-hull distance |
0.0076
| 0.0862 |
Soma-to-center of gravity distance |
0.0138
| 0.2072 |
Reach—maximum | 0.0522 | 0.3715 |
Straightness | 0.0543 | 0.0755 |
Mean contraction | < 0.0001 | 0.2088 |
Hausdorff dimension |
0.0002
|
0.0123
|
Mean fragmentation |
0.0016
| 0.3353 |
Measure names | Viral-labeled | Alexa-labeled | Biotin-labeled |
---|---|---|---|
Number of stems | 0.1355 | 0.1881 | 0.1440 |
Stem diameter—mean | 0.1712 |
0.0078
|
0.0366
|
Stem diameter—sum | 0.8794 | 0.5099 |
0.0007
|
Stem diameter—maximum |
0.0068
|
0.0097
|
0.0298
|
Stem directionality | 0.1491 |
0.0814
| 0.6311 |
Dendrites—total length |
0.0003
|
0.0689
| 0.1586 |
Dendrite diameter—mean | 0.2036 | 0.6204 |
0.0056
|
Dendrites—longest single path length |
0.0010
| 0.2313 |
0.0009
|
Number of bifurcations |
0.0012
| 0.1020 |
0.0007
|
Local bifurcation angle—mean | 0.2128 | 0.7908 | 0.5166 |
Remote bifurcation angle—mean | 0.2437 |
0.0913
| 0.7735 |
Number of branches |
0.0015
| 0.1663 |
0.0010
|
Branch order—maximum |
0.0812
| 0.0066 |
0.0052
|
Number of tips |
0.0892
| 0.0368 |
0.0040
|
Number of cut tips |
0.0826
| 0.2140 |
0.0004
|
Number of tips—total |
0.0144
| 0.1568 |
0.0003
|
Soma area | 0.8722 |
0.0006
|
0.0408
|
Hull volume | < 0.0001 |
0.0059
| < 0.0001 |
Soma-to-hull distance |
0.0043
|
0.0039
|
0.0011
|
Soma-to-center of gravity distance | < 0.0001 | < 0.0001 |
0.0613
|
Reach—maximum |
0.0019
| 0.2754 |
0.0099
|
Straightness |
0.0349
| 0.3158 |
0.0946
|
Mean contraction |
0.0453
|
0.0892
| 0.1451 |
Hausdorff dimension |
0.0545
| 0.5955 | 0.1031 |
Mean fragmentation |
0.0101
| 0.6274 |
0.0132
|
Subjective class | Virus | Alexa | Biocytin | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Min | Median | Mean | Max | Min | Median | Mean | Max | Min | Median | Mean | Max | |
Number of stems | 3 | 6 | 6.03 | 11 | 2 | 4 | 4.63 | 8 | 3 | 7 | 6.45 | 9 |
Stem diameter—mean | 0.68 | 2.16 | 2.17 | 3.22 | 1.17 | 1.75 | 1.97 | 3.88 | 1.67 | 2.5 | 2.49 | 3.95 |
Stem diameter—sum | 6.11 | 12.7 | 12.55 | 18.93 | 4.6 | 8.6 | 8.94 | 15.5 | 10.2 | 15.13 | 16.98 | 32.6 |
Stem diameter—maximum | 1.46 | 3.5 | 3.32 | 4.67 | 1.6 | 2.5 | 2.66 | 5.1 | 2.2 | 3.33 | 3.62 | 5.1 |
Stem directionality | 0.12 | 0.3665 | 0.41 | 0.865 | 0.127 | 0.384 | 0.42 | 0.749 | 0.131 | 0.458 | 0.46 | 0.881 |
Dendrites—total length | 1260 | 2311 | 2634.67 | 7006 | 372 | 1328 | 1423.93 | 3458 | 860 | 2974 | 3098.48 | 5764 |
Dendrite diameter—mean | 0.81 | 2.045 | 2.05 | 3.45 | 1.1 | 2.5 | 2.46 | 4.1 | 1.53 | 2.83 | 2.98 | 5.87 |
Dendrites—longest single path length | 170 | 330 | 367.69 | 906 | 92 | 268 | 295.56 | 523 | 257 | 436 | 468.52 | 1076 |
Number of bifurcations | 6 | 16.5 | 20.22 | 43 | 3 | 8 | 9.11 | 17 | 3 | 12 | 12.48 | 31 |
Local bifurcation angle—mean | 61.4 | 74.95 | 74.96 | 89.4 | 41.8 | 65.8 | 70.11 | 97.7 | 48 | 73 | 73.10 | 98.3 |
Remote bifurcation angle—mean | 58.5 | 84.2 | 84.04 | 107.8 | 26.2 | 87.6 | 84.00 | 114.9 | 49.6 | 90.3 | 86.82 | 122.3 |
Number of branches | 14 | 34.5 | 42.78 | 90 | 8 | 20 | 21.11 | 40 | 8 | 28 | 29.62 | 68 |
Branch order—maximum | 3 | 6 | 6.81 | 13 | 2 | 4 | 4.67 | 9 | 3 | 4 | 4.72 | 9 |
Number of tips | 1 | 10.5 | 11.94 | 33 | 0 | 7 | 8.04 | 19 | 3 | 12 | 12.66 | 31 |
Number of cut tips | 0 | 7 | 6.08 | 11 | 0 | 4 | 3.59 | 9 | 1 | 3 | 3.76 | 13 |
Number of tips—total | 9 | 16.5 | 18.03 | 38 | 5 | 11 | 11.63 | 23 | 6 | 16 | 16.41 | 35 |
Soma area | 112 | 188 | 195.04 | 304 | 97 | 124 | 131.19 | 242 | 150 | 246 | 252.69 | 444 |
Hull volume (104 µm3) | 13.99 | 49.00 | 121.050 | 2062.270 | 6.930 | 49.24 | 60.25 | 160.13 | 23.53 | 115.07 | 192.64 | 1293.82 |
Soma-to-hull distance | 0 | 11.621 | 14.55 | 51.332 | 0 | 6.218 | 6.64 | 24.628 | 0 | 7.258 | 10.54 | 37.675 |
Soma-to-center of gravity distance | 8.445 | 30.697 | 37.67 | 133.654 | 8.912 | 30.76 | 52.69 | 201.59 | 7.417 | 51.762 | 59.69 | 131.578 |
Reach—maximum | 65 | 121 | 139.53 | 265 | 35 | 154 | 145.56 | 298 | 95 | 165 | 183.62 | 420 |
Straightness | 0.129 | 0.368 | 0.42 | 0.813 | 0.19 | 0.49 | 0.51 | 0.81 | 0.21 | 0.39 | 0.40 | 0.79 |
Mean contraction | 0.59 | 0.695 | 0.71 | 0.83 | 0.53 | 0.68 | 0.69 | 0.79 | 0.5 | 0.6 | 0.61 | 0.8 |
Hausdorff dimension | 1.05 | 1.18 | 1.20 | 1.47 | 1 | 1.1 | 1.11 | 1.28 | 1.06 | 1.14 | 1.16 | 1.3 |
Mean fragmentation | 43.8 | 86.75 | 92.12 | 173.6 | 43.5 | 73.5 | 76.04 | 115 | 54 | 96.6 | 97.60 | 184.1 |
Measure names | Correlations to subjective classification | Correlations to straightness | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Viral-labeled | Alexa-labeled | Biotin-labeled | Viral-labeled | Alexa-labeled | Biotin-labeled | |||||||
Rho |
p
| Rho |
p
| Rho |
p
| Rho |
p
| Rho |
p
| Rho |
p
| |
Subjective class | − 0.71 | < 0.0001 | − 0.83 | < 0.0001 | − 0.50 |
0.005
| ||||||
Number of stems | 0.31 | 0.067 | 0.51 |
0.007
| 0.36 | 0.055 | − 0.41 |
0.013
| − 0.60 |
0.001
| − 0.12 | 0.536 |
Stem diameter—mean | − 0.30 | 0.080 | − 0.35 | 0.075 | − 0.32 | 0.089 | 0.58 |
0.000
| 0.42 |
0.030
| 0.15 | 0.428 |
Stem diameter—sum | − 0.08 | 0.661 | 0.23 | 0.254 | − 0.35 | 0.067 | 0.14 | 0.411 | − 0.10 | 0.608 | 0.31 | 0.104 |
Stem diameter—maximum | − 0.22 | 0.210 | − 0.32 | 0.103 | − 0.18 | 0.361 | 0.24 | 0.158 | 0.37 | 0.058 | 0.11 | 0.567 |
Stem directionality | 0.37 |
0.027
| 0.00 | 0.996 | 0.11 | 0.563 | − 0.11 | 0.538 | − 0.09 | 0.664 | − 0.13 | 0.492 |
Dendrites—total length | 0.52 |
0.001
| 0.32 | 0.106 | − 0.02 | 0.915 | − 0.47 |
0.004
| − 0.25 | 0.212 | 0.12 | 0.544 |
Dendrite diameter—mean | − 0.41 |
0.014
| − 0.69 | < 0.0001 | − 0.28 | 0.145 | 0.53 |
0.001
| 0.52 |
0.005
| 0.47 |
0.011
|
Dendrites—longest single path length | 0.33 | 0.051 | − 0.09 | 0.660 | − 0.16 | 0.399 | − 0.53 |
0.001
| 0.02 | 0.906 | − 0.19 | 0.328 |
Number of bifurcations | 0.60 | < 0.0001 | 0.50 |
0.008
| 0.33 | 0.085 | − 0.69 | < 0.0001 | − 0.31 | 0.112 | − 0.25 | 0.192 |
Local bifurcation angle—mean | − 0.07 | 0.702 | − 0.26 | 0.194 | − 0.29 | 0.132 | − 0.13 | 0.459 | 0.50 |
0.008
| − 0.11 | 0.554 |
Remote bifurcation angle—mean | 0.28 | 0.095 | 0.33 | 0.096 | 0.05 | 0.815 | − 0.26 | 0.119 | − 0.41 |
0.034
| − 0.14 | 0.466 |
Number of branches | 0.62 | < 0.0001 | 0.54 |
0.004
| 0.36 | 0.052 | − 0.70 | < 0.0001 | − 0.38 | 0.051 | − 0.19 | 0.334 |
Branch order—maximum | 0.51 |
0.002
| 0.19 | 0.345 | 0.10 | 0.592 | − 0.74 | < 0.0001 | 0.01 | 0.972 | − 0.43 |
0.020
|
Number of tips | 0.73 | < 0.0001 | 0.69 | < 0.0001 | 0.48 |
0.008
| − 0.67 | < 0.0001 | − 0.54 |
0.004
| − 0.42 |
0.025
|
Number of cut tips | − 0.40 |
0.017
| − 0.30 | 0.125 | − 0.22 | 0.254 | 0.40 |
0.015
| 0.21 | 0.298 | 0.39 |
0.036
|
Number of tips—total | 0.65 | < 0.0001 | 0.68 | < 0.0001 | 0.32 | 0.091 | − 0.63 | < 0.0001 | − 0.54 |
0.003
| − 0.26 | 0.173 |
Soma area | 0.15 | 0.391 | 0.04 | 0.855 | − 0.15 | 0.426 | − 0.04 | 0.816 | 0.05 | 0.806 | 0.29 | 0.131 |
Hull volume | − 0.42 |
0.010
| − 0.43 |
0.024
| − 0.48 |
0.008
| 0.50 |
0.002
| 0.45 |
0.017
| 0.49 |
0.007
|
Soma-to-hull distance | − 0.02 | 0.910 | 0.24 | 0.225 | − 0.07 | 0.713 | − 0.12 | 0.504 | − 0.23 | 0.249 | 0.09 | 0.649 |
Soma-to-center of gravity distance | − 0.47 |
0.004
| − 0.63 | < 0.0001 | − 0.41 |
0.026
| 0.48 |
0.003
| 0.67 | < 0.0001 | 0.40 |
0.034
|
Reach—maximum | − 0.54 |
0.001
| − 0.72 | < 0.0001 | − 0.52 |
0.004
| 0.71 | < 0.0001 | 0.80 | < 0.0001 | 0.68 | < 0.0001 |
Straightness | − 0.71 | < 0.0001 | − 0.83 | < 0.0001 | − 0.50 |
0.005
| ||||||
Mean contraction | − 0.60 | < 0.0001 | − 0.79 | < 0.0001 | − 0.58 |
0.001
| 0.57 | < 0.0001 | 0.77 | < 0.0001 | 0.44 |
0.016
|
Hausdorff dimension | 0.58 | < 0.0001 | 0.43 |
0.026
| 0.36 | 0.058 | − 0.69 | < 0.0001 | − 0.44 |
0.021
| − 0.19 | 0.334 |
Mean fragmentation | 0.05 | 0.778 | 0.57 |
0.002
| − 0.01 | 0.974 | − 0.12 | 0.491 | − 0.56 |
0.002
| − 0.08 | 0.691 |