Use cases and result interpretation for the Compartments pipeline operation.
Using compartments operation
What does the Compartments operation do?
In a nutshell, it establishes relationships between objects, assigning children and parent links, and permits the analysis of those relationships.
A Parent-Child relationship is a hierarchical structure where some objects belong to other objects and vice versa. The individual objects have their own characteristics (volume, surface area, intensity), but also features dependent on those relationships (ID of the parent, number of children). The Compartments operation is specifically concerned with establishing the relationships between parent segments and their children. Other types of parents exist, such as tracks or groups, but the compartments operation is specifically concerned with the overlap or proximity of different object types.
Example uses of the Compartments operation
Establishing parent/child relationships can be valuable in a variety of cases, such as:
- Counting foci in nuclei or vesicles inside cells
- Quantifying migration of objects to or from the inside of cells
- Measuring the numerical density of cells inside specific brain regions
In each of these cases, the number and size of the objects of interest are relevant based on their position relative to a parent.
Configuring the Compartments operation in a pipeline
The first thing that is needed before adding the compartments operation is a set of parent and children objects. Since many segmentation methods can result in unwanted objects it is also best to use any object filtering operation prior to adding the Comparmtnets operation to the pipeline.
The compartments operation can the be added to the pipeline like any other operation.
Once added to the pipeline we can configure the operation parameters.
Compartment operation inputs
Each Compartments operation can have one Parent object tag and multiple children object tags. If there are several potential parent objects in your pipeline, either multiple Compartments operations must be used (one for each parent type), or the parents must be given a common tag with the Combine Segment Outputs operation. The tag to be used for the parents can be selected from previous pipeline tags.
Parents can have multiple children tags. When added to the pipeline the operation starts with one parent and one child tag. To add another child object tag we can just click "+ Add input" and select from the available object tags. Note that the children cannot be either the parents or a subset thereof.
Conclusions
The Compartments operation, together with the objects tables and features, can provide powerful insights into object relationships in image analysis. Unfortunately, it is difficult to do this topic justice in a knowledge base article due to the vast array of potential uses and applications where these tools can be used. Hopefully, this article provides a valuable overview. Please contact support using the link at the top of the page if you require any additional help with your analysis.