📄️ Threshold
In the Threshold menu, select any number of variables for analysis with Phenoplex.
📄️ 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.
📄️ Phenotype List
This section provides a description of the Phenotype List, where identified phenotypes can be managed and reviewed. The list shows the identified cell populations color coded by phenotype. It serves as a central repository for all phenotypic data.
📄️ Neighbor Counts
The Neighborhood count feature is used for neighborhood analysis. In Neighbor Counts you are able to quantify the number of neighboring cells for each phenotype. This feature is available in version 2024.06 Beta and newer, and it is helpful in understanding cell-to-cell interactions within the tissue.
📄️ Nearest Neighbor
The feature Nearest Neighbor in the Phenoplex Guided Workflow can be used to understand the spatial relationships between specific biomarker-positive targets and neighboring objects within a defined distance.