Measuring how often and how long some objects come into contact with each other can be a useful tool in biological relationship analysis. This guide explains how grouping combined with tracking can provide this information.
Time lapse analysis
Quantifying contacts over time
Tagging contact events
Once both types of objects have been identified (more can be added if needed), the next step is to identify points of interaction. This can be based on proximity (if a subject-object is within a certain distance of a reference-object), or overlap (if part or whole of a subject-objects is within the bounds of a reference-object).
The distance operation can be used if a specified distance is enough.
In this case, we have configured the operation in the following way:
- Renamed the operation so the tag attached to the objects is "contact" for ease of reading the pipeline and results.
- Set the operation to change the colour of tagged objects to Cyan to easily spot interactions in the viewer.
- Set the subject to be the objects that will be tracked and whose interaction we want to measure and set the reference be those the subjects come into contact with.
- Set the filter to be a distance below 2um. The distance, in this case, was set to be fairly generous due to the processing and segmentation of the objects, but it can be set to any value as needed, even 0, meaning that objects must touch for an interaction to be inferred.
- Set the distance calculation to be based on the proximity of the geometries of both the subjects and references.
- While the option to store the distance feature is on, it is unnecessary for the purpose of tagging.
Alternative ways to tag contact can also work. If the Distances operator is unpractical because it is too much computing for the image using a distance map is absolutely fine. Also, it is possible to use the Compartments operation if contact is limited to the overlap of objects.
Interpreting the data
Having tracked the objects, there are a few things that can be done to help interpret the data and extract the required information. Most of it is done from the Objects table.
Custom Features
Finally to get the number of interaction we can create a custom feature for the number of track children with the tag "Contact".
We Start by opening the Custom Features editor and adding a new Group Statistics feature.
This new custom feature has been configured as follows:
- The name is set to reflect the data it represents. In this case, the number of children objects that make contact.
- The Feature on which this custom is configured has been set to the number of children (# Children).
- The Tag field has been set to only include objects with the tag "Contact".
- The value that is added as a column in the table is the Count.
When finished the number of children that make contact will appear in the objects table as a feature of the tracks.
This feature can also be added as a feature filter for the tracks to quickly get a count of tracks that make contact.
Source: Image courtesy: Dr. B. Stolp, Heidelberg University, Center for Integrative Infectious Disease Research (CIID)