Co-occurrence Matrix

The co-occurrence matrix helps the user to identify and QC pairs of biomarkers which should, and should-not co-occur within cells. This can help to identify problems all the way from sample preparation through cell segmentation, to phenotyping. For any row and column in the matrix, the numbers are the total number of cells positive for both biomarkers, across all the images loaded into the guided workflow.

caution

Make sure to select the variables and check the Use for phenotyping box in the Threshold menu before proceeding to the Co-occurrence Matrix.

Co-occurence matrix showing that Ki67 and EpCAM co-occours 278 times

Clicking on one of the co-occurrence numbers will show where they are on the current image. Clicking in the same field again hides the yellow positivity marker dots in the viewer.

Double positive objects are indicated in the image with a yellow dot

tip

Data from the co-occurrence matrix can be copied into Excel using the standard shortcuts Ctrl+C and Ctrl+V.