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Colocalization

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USE CASE

Identify Relationships Using Colocalization

The Colocalization operator is ideal for finding relationships between objects, in a one to any relationship. This allows for sophisticated measurements of a group created between a “parent” and “child” objects. The enhanced Colocalization allows groups to be created from a reference (parent) and subjects (child) based on position. As part of the Analysis Pipeline it allows for the easy segmentation and subsequent quantitative analysis of cells, spheroids, nuclei or any other type of rounded cell organelles, even in crowded and noisy environments in 2D, 3D and 4D data sets. This operator requires two groups of objects, references and subjects, to find relationships between the groups.

STEP 1

Identify Objects Diameter

arivisVision4D-colocalization1-min

 

Use Segment generation operators (Intensity Threshold, Blob Finder, and Membrane Segmenter) to identify the objects or cells of interest.

STEP 2

Filter Threshold

Add a Segment Filter to exclude over segmented and unwanted objects, or incorrectly detected objects.

arivisVision4D-colocalization2-min

 

STEP 3

Setup Segment Colocalization Operator

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Now add the ‘Segment Colocalization” operator, and set the subject and references. The “Subjects” will become the “Child” of the “Reference” parent, when the ‘colocalize entities by group” Is selected. This is a big change from the previous “by tag” option. The group function allows per group statistics to be created in the ‘Custom Features’ panel.

Results

Before

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After

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The segment Colocalization can select the subjects that meet the Coloc-measure, by complete coverage, partial coverage, or a user specified distance to the shape of the subjects.

arivisVision4D-colocalization6-min

 

arivisVision4D-colocalization7-min

 

Use the objects table to see sequentially numbered object groups, cell-groups in this example.
New features include number of children, and all child (subject) IDs, this is very important for tracking interactions between different groups in a time series. Use the “Drill Down” option to examine the contents of groups, to see each individual subjects  
Use the Import/Export functions to export the grouped data into convenient excel or csv files. The master-detail option puts the group data in a special excel page or separate csv file, and then each individual group gets its own page or file.

arivisVision4D-colocalization8-min