Plot the SWC features in tSNE/UMAP

[JohnTigue]

Cell Types whitepaper, page 12

Reconstructions were saved in the SWC file format, which is a widely used ASCII format for specifying neuronal morphology (e.g., used by neuromorpho.org (Ascoli et al., 2007)). Multiple morphological features were selected for analysis based on these reconstructions. Extracted features provide data input for the generation of a morphology-based taxonomy, and will be integrated with taxa from other neuron attributes such as electrophysiology or transcriptomics.

Extracted features included twenty-one global morphology metrics. A subset of morphology features defined in L-Measure (http://cng.gmu.edu:8080/Lm/help/index.htm) (Scorcioni et al., 2008) were produced in the informatics pipeline by the Vaa3D plugin “Compute Global Features” (Table 6). To see descriptive images of the Morphology Features (except number of nodes) for dendrites only, hover over the name to follow the hyperlink embedded in the text.

[JohnTigue]

Table 6, on page 13:

Morphological	Feature Definition
Number of nodes	The total number of nodes in the given input neuron (one SWC file). A node in a SWC file represents a single sample point of the neuron defined by its X, Y and Z coordinates, a radius, and its connectivity to other nodes in the neuron.
Soma surface area	The surface of the soma is computed by one of two methods. If the soma is composed of just one node then the sphere assumption is used; otherwise the sum of the external cylindrical surfaces of nodes forming the soma is calculated.
Number of stems	The number of stems attached to the soma. When the type of the node is not soma, it is labeled as a stem.
Number of bifurcations	The number of bifurcations for the given input neuron. A bifurcation point has two daughters.
Number of branches	The number of branches in the given input neuron. A branch is one or more compartments that lie between two branching points or between one branching point and a termination point.
Number of tips	The number of terminal tips for the given input neuron. This function counts the number of nodes that are terminal endpoints.
Neuronal height	Height is computed on the y-coordinates and it is the difference of minimum and maximum y-values after eliminating the outer points on either end by using the 95% approximation of the y-values of the given input neuron.
Neuronal width	Width is computed on the x-coordinates and it is the difference of minimum and maximum x-values after eliminating the outer points on either end by using the 95% approximation of the x-values of the given input neuron.
Neuronal depth	Depth is measured on the y-coordinates and it is the difference of minimum and maximum y-values after eliminating the outer points on either ends by using the 95% approximation of the y-values of the given input neuron.
Average diameter (thickness)	The average diameter of all compartments of the neuron.
Total length	The total length of the neuron is computed as the sum of distances between two connected nodes for all branches of the input neuron.
Total surface area	The total surface area of the entire neuron.
Total volume	The total volume of the entire neuron.
Maximum Euclidean distance to root	The maximum Euclidean distance of all nodes. Euclidean distance is the straight line distance from the soma (root) to the node.
Maximum path distance to root	The maximum path distance of all nodes. The path distance is the sum of lengths of all connected nodes from the soma, ending with that node.
Maximum branch order	The maximum order of the branch. A branch’s order is defined with respect to the soma where the soma has a branch order = 0. The first bifurcation has a branch order = 1, the second bifurcation has a branch order = 2, and so on.
Average contraction	The average ratio between Euclidean distance of a branch and its path length. Euclidean distance of a branch is the straight-line distance from the soma to the branch. Path length is the sum of the lengths between each node along the path.
Average fragmentation	The average number of compartments that constitute a branch between two bifurcation points or between a bifurcation point and a terminal tip.
Average parent-daughter ratio	The average ratio between the diameter of a daughter branch and its parent branch. One value for each daughter branch is generated at each bifurcation point.
Average local amplitude angle	The average angle between the first two compartments (in degree) at a bifurcation.
Average remote amplitude angle	The average angle between two bifurcation points or between bifurcation point and terminal point or between two terminal points.