Varicosities (branched structure analysis)

Neurolucida 360 software only

Purpose

Use the Varicosities analysis to generate quantitative data about the varicosities and how they are situated on neuronal processes.

Metrics are generated based on a 5-point representation of each varicosity.

Analysis results

Varicosity details

Tree: Each tree selected for the analysis is assigned a unique number starting at 1.

Branch order: Uses the centrifugal branch order. See About branch orders.

Maximum diameter: Diameter at the center (i.e., middle point) of the varicosity.

Length: Distance between the first point and the last point of the 5-point segment.

Thickness ratio: The diameter at the center of the varicosity multiplied by its image intensity at that location, divided by the diameter of the underlying tree (measured just outside the varicosity) multiplied by its image intensity.

Distance to root: Sum of the branch segments from the center (i.e., middle point) of the varicosity to the beginning (root) of the tree the varicosity is assigned to.

Distance along branch: Sum of the branch segments from the center (i.e., middle point) of the varicosity to the closest node.

Volume: Measured by the number of voxels that make up the varicosity object multiplied by the volume of a single voxel. The volume of a single voxel is: X resolution * Y resolution * Z resolution.

Surface area: Based on the mesh used to represent varicosities.

Base coordinate: 3D coordinate (X,Y,Z) of the point where the varicosity is attached to the dendrite.

Dendrite/Apical dendrite/Axon varicosity

Tree: Each tree selected for the analysis is assigned a unique number starting at 1.

Total #: Number of varicosities on this segment.

Density: [Quantity of varicosities on the segment]/[Length of the segment]

Average varicosity diameter: Average diameter of the varicosities on the segment.