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Many of the analyses report branch order or depend on branch order in the grouping of branched structure segments. The default branch order in Neurolucida is centrifugal (see Branch ordering in Neurolucida for details).
A branched structure such as a dendrite is organized in a form known as a tree.
A tree is a connected structure that branches, but has no loops.
Segments, also called branches, are the parts of the tree that connect terminations (endings) or nodes.
One termination is special: the starting point of the tree, called the root.
Dendrites and axons are considered to be rooted trees with an origin at the cell body. A basic understanding of dendrites and axons involves the manner in which they branch.
Numbers are assigned to branches to describe the hierarchy of the branching scheme. The numbering scheme is called the branch order for the tree.
Neurolucida Explorer uses the following Branch Ordering schemes: Centrifugal, Centripetal, Strahler, Terminal Distance, Microvascular Branch, Shaft.
Centrifugal ordering begins at the origin of the tree and works out towards the terminations. Other ordering schemes begin at the terminations and work towards the origin or root of the tree. The Centripetal , Strahler, and Terminal Distance ordering methods begin labeling at the terminations.
The centrifugal method is the basic scheme to assign branch order to a tree.
This process continues until all branches are assigned a value.
Centrifugal ordering counts the distance from the root in terms of the number of segments traversed. The advantage to centrifugal ordering is that missing portions of the tree do not result in incorrect numbering of the known segments.
The centripetal method starts with zero at each terminal segment, and proceeds towards the root.
This continues until the segment attached to the root is reached.
The order of a branch is the topological distance (number of nodes to cross) downwards to the farthest terminal branch.
Therefore, the order of the root branch is the depth of the tree minus 1.
The maximum centripetal order "+1" is the same as the maximum centrifugal ordering of the tree.
The centripetal ordering is similar to retrograde maximal ordering; it is referred to as diameter order or Horsfield order in the literature.
The Strahler method also begins the numbering scheme by assigning the order "0" to all of the terminal segments
The Strahler ordering method increases the order if the daughter segments are balanced trees.
If the daughter segments are not balanced, however, it is the part of the tree that had the most balance that is used as the order number. Unlike the previous ordering schemes, Strahler ordering does not use a topological distance property.
The terminal distance ordering begins at the terminal segments and works towards the root.
The order of a segment is the topological distance (number of nodes to cross) downwards to the closest terminal branch. Therefore the order of the root segment is the minimal depth of the tree. This contrasts with the Centripetal ordering that is the maximum distance.
The terminal distance ordering is similar to retrograde minimal ordering.
Microvascular branch ordering is based on vessel diameter and branching order.
In general, when a parent vessel splits:
The specific rules and exceptions are as follows:
Shaft order is only displayed in Neurolucida Explorer if it has been previously assigned in Neurolucida (See Branch Ordering in Neurolucida)
Shaft ordering recognizes that the tree is dominated by one main path and that all other portions of the tree are subsidiary to the main path. The main path can be changed, resulting in a re-numbering of the tree.
As shown below, all segments along the primary branch are designated with a "1."
Uylings, H. B., Smit, G. J., & Veltman, W. A. (1974). Ordering methods in quantitative analysis of branching structures of dendritic trees. Advances in Neurology, 12, 347-354.
Uylings, H. B. M., Ruiz-Marcos, A., & Van Pelt, J. (1986). The metric analysis of three-dimensional dendritic tree patterns: a methodological review. Journal of Neuroscience Methods, 18(1), 127-151.
To modify branch order options:
To visualize your structures by branch order:
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