This is a repository for the CellOntology plugin for FlowJo client.
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Almost all applications in flow cytometry rely on phenotype markers to identify specific cell types and their associated functions, etiologies, or biological contexts. Using the CellOntology plugin, you can query the CellOntology database and its published definitions of cell types and phenotypic markers to identify the cell or population you have in the FlowJo workspace.


The CellOntology plugin is included with FlowJo v10.1r7 and later. Like all plugins, it requires that version or later to run.

CellOntology is implemented as a program in the R statistical computing environment. Therefore, to use CellOntology, you must install R and the required R packages onto your computer. To install R on your computer, see the Installing Plugins page on the FlowJo documentation site. Once R is installed, you will no longer need to open R to access CellOntology in FlowJo.

Installation Instructions

The CellOntology plugin is included with FlowJo.

If you need to update or re-install CellOntology, please see the Installing Plugins page for detailed information on how to obtain and set up FlowJo plugins.


For more detailed instructions on how to use CellOntology, refer to the CellOntology page on the FlowJo documentation site.