FlowJo

FlowJo is a commercial software package for analyzing flow cytometry data. It provides a graphical interface for inspecting multivariate cytometry measurements, enabling users to import FCS files from flow cytometers, define gates to identify cell populations, and compute statistics such as percentages, mean fluorescence intensity, and population frequencies.

The program supports compensation for spectral overlap, visualization of data through plots such as biaxial scatter plots, histograms, violin plots, and density plots, and it can export figures and data for downstream analysis.

FlowJo organizes analyses into workspaces that store gating trees, sample metadata, compensation matrices, and analysis templates. This enables users to apply consistent gating strategies across large datasets and to batch-process samples. It supports linking multiple samples, time-course experiments, and export of gated populations. FlowJo also offers automation features to streamline repetitive tasks and to generate standardized reports.

The software runs on Windows and macOS and works with common flow cytometry file formats, especially FCS, including support for compensation matrices and spectral cytometry data.

It is widely used in immunology, cancer biology, stem cell research, and clinical laboratory settings for data exploration, quality control, and standardized reporting.

FlowJo originated in the late 1990s under Tree Star, Inc. and has since evolved through several version updates and branding changes. It remains one of the most widely adopted tools for flow cytometry data analysis.