Measuring a path

The path measurements include:

Nodes labeling and classification

For measurement purposes the nodes that comprise a path are labeled and classified.

For each Object with a path defined, isolated sub-paths are determined. A sub-path is a set of connected nodes, that are not connected with others sub-paths. Figure 1 shows a path comprised of connected nodes, and Figure 2 shows a path comprised of two isolated sub-paths.

For each sub-path the process determines:

The nodes that do not meet the preceding criteria are intermediate nodes, and they are not taken into account for measurement purposes (in this version of BioVis3D).

Each path is labeled starting with number 1, the sequence will then follow the number of nodes in the path. The root node of each sub-path is labeled with the consecutive number as of the last node labeled in the previous sub-path processed. 


Figure 1: Path comprised of connected nodes The node labeled 1 is the root node (it has one connection), the node labeled 2 is a branch node (it has 3 connections), and the nodes labeled 3 and 4 are terminals nodes (they have 1 connection).

 


Figure 2: Path comprised of two sub-paths Each sub-path is comprised of connected nodes, being that the sub-paths are not connected. The second sub-path is labeled starting in number 5, because the preceding sub-path finishes in 4. The node labeled 5 is the root node of the second sub-path, the node labeled 6 is a branch node, and the nodes labeled 7 and 8 are terminals nodes.


Figure 3: Intermediate nodes of the path Note that the intermediate nodes (the ones not classified as root, branch or terminal, shown in the figure with colors green and yellow) do determine the trace of the path, but they are not labeled, they are not shown in the 3D View, and they are not taken into account for measurement purposes.

Parent node and child nodes: Each path is subdivided into sub-paths, where each sub-path is a tree, with a root arbitrary selected. Each node has a parent node (not in the case of the root node), and it could have child nodes. In Figure 3, the branch node labeled 2 has the parent node 1, and the child nodes 3 and 4.

Measuring

Measuring is done for the nodes classified as root, branch or terminal (intermediate nodes will be considered in future versions of BioVis3D).

The measurements are exported to a tab-separated text file, with extension .TXT that can be imported by a spreadsheet or scientific application, or opened with a text editor. To export paths measurements see Export Sequence.

The following information is measured and exported:

  • For each node classified as root, branch or terminal: 

      - the node label
      - the node type (root, branch, terminal)
      - the number of connections
      - the node diameter
      - the node position (in the unit of measure of the sequence, and in pixels)

    Table 1 shows the exported information opened and formatted with a spreadsheet application.


    Table 1: Information about the nodes

  • For each node classified as branch and for each correspondent child node: 

      - the three-dimensional Euclidean distance between the branch node and the child node (note that the length of the trace between the branch node and the child node is not measured).
      - the angle between the parent node of the branch, the branch node and the child node. The angle is expressed in degrees.

    Table 2 shows the exported information opened and formatted with a spreadsheet application.  


    Table 2: Information of the branch-child

  • For each node classified as branch and for its correspondent pairs of child nodes: 

      - the angle between one child node, the parent node, and a second child node. The child nodes are selected by pairs, from the lowest label to the highest one as follows: if the branch node 2 has four children, labeled 3, 4, 5 and 6, the angles measured would be 3-2-4, 4-2-5, 5-2-6. The angle is expressed in degrees.

    Table 3 shows the exported information opened and formatted with a spreadsheet application. 


    Table 3: Information about the branch-child pairs