Open JohnTigue opened 4 years ago
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. |
Cell Types whitepaper, page 12