FlowJo is a powerful and user-friendly software for analyzing flow cytometry data, developed by FlowJo, LLC (now part of BD Life Sciences). It is widely regarded as the industry standard for processing, visualizing, and interpreting flow cytometry data, offering advanced tools for both basic and high-dimensional analyses. FlowJo supports various file formats (such as FCS, LMD, CSV) and integrates with mass cytometry (CyTOF), spectral flow cytometry, and single-cell RNA sequencing (scRNA-seq). Its visual interface, customizable workflows, and robust statistical tools make it essential for researchers in immunology, oncology, and cell biology.
Data Visualization and Gating
Interactive hierarchical gating for identifying populations (e.g., lymphocytes, monocytes, tumor cells).
Advanced plotting capabilities.
Immunophenotyping and Biomarker Analysis
Quantification of immune cell subsets using surface markers (e.g., CD4+/CD8+ T cells, B cells, NK cells).
Cell Cycle and Proliferation Analysis
Modeling DNA content (PI/DAPI) to determine G0/G1, S, and G2/M phases.
Tracking proliferation with CFSE/Ki-67.
Functional Assays
Analysis of intracellular cytokine staining (ICS) (e.g., IFN-γ, TNF-α).
Studies on calcium flux, phosphorylation, and apoptosis (Annexin V/PI).