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Version: 2025.08-beta

Phenotype List

This section provides a description of the Phenotype List, where identified phenotypes can be managed and reviewed. It serves as a central repository for all phenotypic data. The Phenotype list offers an overview of the selected Variables and their co-occurrences. It also displays the Cell count of the individual phenotypes and their co-occurrences. Visibility can be toggled by clicking on the eye next to the Cell count.

Cells postive for selected stains shown in color, other cells shown in grey (Lung cancer tissue IMC).
Cells postive for selected stains shown in color, other cells shown in grey (Lung cancer tissue IMC).

Phenotype Naming and Sorting

This feature introduces a standardized, alphanumeric naming and sorting system for phenotype classification, ensuring that biomarker combinations are displayed in a logical and consistent order. This update simplifies phenotype identification and improves readability, particularly in complex tasks involving multiple biomarkers.

Alphanumeric Naming

Phenotype names are generated by concatenating biomarker names in a strict alphanumeric order, regardless of the functional category or biological significance of each marker. For instance, a phenotype containing CD3, CD8, CD40, and PD-L1 will always be displayed as CD3+ CD8+ CD40+ PD-L1+, rather than reflecting the order in which biomarkers were labeled.

Layered Sorting

Negative Phenotypes: If applicable, these are displayed first in the phenotype list. Single Positives: Phenotypes with single positive markers are listed next, sorted alphanumerically. Double Positives, Triple Positives, etc.: As the complexity of the phenotype increases, phenotypes are sorted in ascending alphanumeric order within each group.

Alphanumerical ordering of phenotypes and their names
Alphanumerical ordering of phenotypes and their names

Export phenotypes to Database

Selecting Export to Database adds a new dataset containing all cells and their phenotypes:

Export phenotypes to Database
Export phenotypes to Database

Export to TSV file

Clicking on Export list to TSV file will export the phenotype list as a .tsv to any specified folder. This can then be used in the Explore Q/C tool to explore and uncover differences between cohorts.