Segment (branched structure analysis)

Purpose

Use Segment analysis to obtain the finest details for branched structure analysis. A segment is defined as any portion of a branched structure with endings that are either nodes or terminations with no intermediate nodes.

Analysis results

Tree: Each dendrite selected is assigned a unique number beginning with 1.

Order: Branch order of the segment. About branch orders

  • To select additional branch ordering methods, go to Preferences in the File menu and select Ordering and select the desired branch orderings from the Analysis Branch Orderings list.
  • To obtain shaft data, assign Shaft ordering to your tracing while working in Neurolucida or Neurolucida 360 (see Branch Ordering in the Neurolucida or Neurolucida 360 user-guide).

Segment: Each segment on a dendrite is assigned a unique number beginning with 1. The segment ID number is preceded by the dendrite ID number that the segment belongs to.

Classification: The classification assigned to the segment while working in Neurolucida 360. If no classification was assigned, the cell will be blank.

Length (µm): Total length of the line segments used to trace the segment.

Tortuosity: Tortuosity = [Actual length of the segment] / [Distance between the endpoints of the segment]

  • The smallest possible tortuosity value is 1. This indicates a straight path.
  • Tortuosity increases as the segment assumes a more complex path to reach its destination.
  • Tortuosity allows segments of different lengths to be compared in terms of the complexity of the paths they take.

Surface Area (µm²)/ Volume (µm³): Computed by modeling the pieces of the segments as frusta (i.e., truncated right circular cones).

Terminal Type: Describes the end point of the segment that is distal to the origin, the most common being Normal and Branch:

  • Normal: Describes a terminal segment point that is the end of a branch.

  • Branch: Describes a terminal segment point that is a node (bifurcating or trifurcating).

 

Normal Ending (N) Default
High Ending (H)

Ending located at the top of the current section. Depending on the orientation of the sections, the process may continue into another section.

  • Use the Z Meter to determine the Z value of the ending.
Low Ending (L) Ending located at the bottom of the current section.
Incomplete (I) Use to label arbitrary endings, endings that disappear for unknown reasons, endings that should be audited later.
Origin Ending (O)

Indicates the directionality of the tree.

  • Use this setting if you have been tracing towards the cell body and find that your "ending" is actually the beginning of the process.

Neurolucida Explorer keeps track of directionality to apply branch orders.

Midpoint (M) Ending of a long branch that is indeterminate at the time it is placed.
Generated (G) When Neurolucida or Neurolucida 360 is unable to determine an ending type, it assigns a "Generated" ending. This can happen during editing when the ending type originally assigned is no longer valid, or a new ending is created. Examples include editing to relocate the origin ending, which leaves the original origin unassigned, or splitting a branch, which creates new endings. You may need to evaluate the generated endings and assign the appropriate ending type.
Branch (B) Describes a terminal segment point that is a node (bifurcating or trifurcating). The Branch ending type will only be seen in segment analyses.

Planar Angle (°): Computed based on the endpoints of the segments. It refers to the change in direction of a segment relative to the previous segment. Consequently, the first segment in a tree does not have a planar angle and is marked N/A.

XY Angle / Z Angle (°): XY and Z angles form the spherical coordinate angles for the end of the first segment relative to the start of the next segment.

Max Angle (°): Defined only for segments that end at nodes. The value is the maximum of the planar angles of the daughter segments (i.e., the other segments that are attached to the node).

Base Diameter (µm): Diameter at the start of the segment.

Avg Diameter (µm): Length-weighted mean. The segment is modeled as a series of frusta. The length of each frustum is used in the calculations to provide a correct average diameter over the length of the segment as it tapers.

Max Diameter (µm): Maximum diameter of the segment.

Min Diameter (µm): Minimum diameter of the segment.

Base Coordinates: The base coordinate is the (X, Y, Z) position of the start of the segment.

Spines: The number of spines present on the segment. The subsequent columns list the number of each spine type if spines were classified while working in Neurolucida or Neurolucida 360.