Module: MeasureObjectNeighbors

Measure Object Neighbors calculates how many neighbors each object has and records various properties about the neighbors' relationships, including the percentage of an object's edge pixels that touch a neighbor.
Given an image with objects identified (e.g., nuclei or cells), this module determines how many neighbors each object has. You can specify the distance within which objects should be considered neighbors, or that objects are only considered neighbors if they are directly touching.

Available measurements

Object measurements

Object relationships: The identity of the neighboring objects, for each object. Since per-object output is one-to-one and neighbors relationships are often many-to-one, they may be saved as a separate file in ExportToSpreadsheet by selecting Object relationships from the list of objects to export.

Technical notes

Objects discarded via modules such as IdentifyPrimaryObjects or IdentifySecondaryObjects will still register as a neighbors for the purposes of accurate measurement. For instance, if an object touches a single object and that object had been discarded, NumberOfNeighbors will be positive, but there will not be a corresponding ClosestObjectNumber.

See also the Identify modules.

Settings:

Select objects to measure

Select the objects whose neighbors you want to measure.

Select neighboring objects to measure

This is the name of the objects that are potential neighbors of the above objects. You can find the neighbors within the same set of objects by selecting the same objects as above.

Method to determine neighbors

There are several methods by which to determine whether objects are neighbors:

For Adjacent and Expand until adjacent, the PercentTouching measurement is the percentage of pixels on the boundary of an object that touch adjacent objects. For Within a specified distance, two objects are touching if their any of their boundary pixels are adjacent after expansion and PercentTouching measures the percentage of boundary pixels of an expanded object that touch adjacent objects.

Neighbor distance

(Used only when "Within a specified distance" is selected)
The Neighbor distance is the number of pixels that each object is expanded for the neighbor calculation. Expanded objects that touch are considered neighbors.

Retain the image of objects colored by numbers of neighbors?

An output image showing the input objects colored by numbers of neighbors may be retained. A colormap of your choice shows how many neighbors each object has. The background is set to -1. Objects are colored with an increasing color value corresponding to the number of neighbors, such that objects with no neighbors are given a color corresponding to 0. Use the SaveImages module to save this image to a file.

Name the output image

(Used only if the image of objects colored by numbers of neighbors is to be retained for later use in the pipeline)
Specify a name that will allow the the image of objects colored by numbers of neighbors to be selected later in the pipeline.

Select colormap

(Used only if the image of objects colored by numbers of neighbors is to be retained for later use in the pipeline)
Select the colormap to use to color the neighbor number image. All available colormaps can be seen here.

Retain the image of objects colored by percent of touching pixels?

Select Yes to keep an image of the input objects colored by the percentage of the boundary touching their neighbors. A colormap of your choice is used to show the touching percentage of each object. Use the SaveImages module to save this image to a file.

Name the output image

(Used only if the image of objects colored by percent touching is to be retained for later use in the pipeline)
Specify a name that will allow the the image of objects colored by percent of touching pixels to be selected later in the pipeline.

Select a colormap

(Used only if the image of objects colored by percent touching is to be retained for later use in the pipeline)
Select the colormap to use to color the percent touching image. All available colormaps can be seen here.