📄️ Threshold
In this section, you will learn how to set and adjust thresholds to differentiate between various phenotypes within your tissue samples. Proper thresholding is crucial for accurate phenotype identification.
📄️ Co-occurrence Matrix
In this section, we will explore the Co-occurrence Matrix, which helps in understanding the spatial relationships between different phenotypes. This matrix is essential for analyzing how phenotypes are distributed in relation to each other within the sample.
📄️ Phenotype List
This section provides a description of the Phenotype List, where you can manage and review the identified phenotypes. It serves as a central repository for all phenotypic data.
📄️ Neighbor Counts
The last feature in the Phenoplex guided workflow is the Neighborhood count feature 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
To help understand the spatial relationships between specific biomarker-positive targets and neighboring objects within a defined distance, the user can use the feature "Nearest Neighbor" in the Phenoplex Guided Workflow.