Module: MeasureNeurons

Measure Neurons measures branching information for neurons or any skeleton objects with seed points.

This module measures the number of trunks and branches for each neuron in an image. The module takes a skeletonized image of the neuron plus previously identified seed objects (for instance, the neuron soma) and finds the number of axon or dendrite trunks that emerge from the soma and the number of branches along the axons and dendrites. Note that the seed objects must be both smaller than, and touching the skeleton in order to be counted.

The typical approach for this module is the following:

The module determines distances from the seed objects along the axons and dendrites and assigns branchpoints based on distance to the closest seed object when two seed objects appear to be attached to the same dendrite or axon.

Available measurements

Settings:

Select the seed objects

Select the previously identified objects that you want to use as the seeds for measuring branches and distances. Branches and trunks are assigned per seed object. Seed objects are typically not single points/pixels but instead are usually objects of varying sizes.

Select the skeletonized image

Select the skeletonized image of the dendrites and/or axons as produced by the Morph module's Skel operation.

Retain the branchpoint image?

Select Yes if you want to save the color image of branchpoints and trunks. This is the image that is displayed in the output window for this module.

Name the branchpoint image

(Used only if a branchpoint image is to be retained)
Enter a name for the branchpoint image here. You can then use this image in a later module, such as SaveImages.

Maximum hole size:

(Used only when filling small holes)
This is the area of the largest hole to fill, measured in pixels. The algorithm will fill in any hole whose area is this size or smaller.

Export the neuron graph relationships?

Select Yes to produce an edge file and a vertex file that give the relationships between trunks, branchpoints and vertices.

Intensity image

Select the image to be used to calculate the total intensity along the edges between the vertices.

Vertex file name

Enter the name of the file that will hold the edge information. You can use metadata tags in the file name.

Each line of the file is a row of comma-separated values. The first row is the header; this names the file's columns. Each subsequent row represents a vertex in the neuron skeleton graph: either a trunk, a branchpoint or an endpoint. The file has the following columns:

Edge file name

Enter the name of the file that will hold the edge information. You can use metadata tags in the file name. Each line of the file is a row of comma-separated values. The first row is the header; this names the file's columns. Each subsequent row represents an edge or connection between two vertices (including between a vertex and itself for certain loops).

The file has the following columns: