Table 3.
Arbor analysesa
| Parameter | Units | Function name | Description |
|---|---|---|---|
| Segment length | µm (real) | segment_length | Length of each segment between branch points |
| Segment number | NA (int) | segment_number | Number of segments between branch points |
| Arbor length | µm (real) | arbor_length | ∑(segment lengths) |
| Tip number | NA (int) | tip_number | Number of terminal dendritic branches |
| Path length | µm (real) | path_length | Length from soma to tip of dendrite |
| Tortuosity | NA (real) | tortuosity | |
| Soma diameter | µm (real) | soma_size | Diameter of sphere fit to soma at widest point |
| Primary arbor number | NA (int) | primary_arbor_number | Number of neurites emerging directly from soma |
| Arbor volume | µm3 (int) | volume | 3D volume of convex hull fit to all arbor nodes |
| Arbor density | µm/ µm3 (real) | density | |
| Arbor directionality and orientation | NA (real) | directionality | |
| (X, Z) directionality and orientation | NA (real) | xz_directionality | Same as directionality using (X, Z) coordinates |
| Radial Sholl | NA (real) | radial_sholl | Number of paths within angle θ from the apical dendrite around the arbor in 30° step |
| Sholl analysis | NA (real) | sholl | Number of segments X distance from soma (20 μm increments reported, customizable) |
| Relative contribution | NA (real) | relative_contribution | ΔA = ΔL(NT1) + ΔN(LT1) + (ΔL)(ΔN) Where A = arbor length, N = segment number, L = mean segment length, and T1= P7 |
aList of each parameter name, unit of measure, function name in custom analysis package, and plain language description of measurement.