FlowJo

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FlowJo is the name of a piece of software for analyzing flow cytometry data. Files produced by modern flow cytometers are written in a standard format called .fcs. Hence FlowJo will import and analyze cytometry data regardless of which FACS (Fluorescence Activated Cell Sorting) machine is used to collect the samples. In FlowJo samples are organized in a "Workspace" window, which presents a hierarchical view of all the samples and their analyses (gates and statistics). Viewing an entire experiment in a Workspace enables you to organize and manage complex cytometry experiments while making detailed graphical reports.

Within a workspace, samples can be grouped or sorted by various attributes such as the panel of antibodies with which they are stained, tissue type, or patient from whom they came. When one performs an operation on a group, FlowJo performs the same operation on every sample belonging to that group. Thus, you can apply a gate to a sample, copy it to a group, and that gate will be automatically placed on all samples in the group.

FlowJo's ability to automate repetitive operations facilitates the production of statistics tables and graphical reports when the experiment involves many samples, parameters and/or operations.

FlowJo provides tools for the creation of:
Histogram and other plot overlays
Cell cycle analysis
Calcium flux analysis
Proliferation analysis
Quantitation
Cluster identification
and backgating display.

Tree Star, Inc. began as a software company in 1989. At that time, the authors' work at Stanford University’s Information Technology department brought them into contact with the Herzenberg Laboratory where modern flow cytometry originated. As the utility and power of cytometers quickly evolved, there arose a need for a more powerful and user-friendly analysis and display program. The development of FlowJo’s graphical user interface made practical the analysis of the extremely voluminous cytometric data.

FlowJo became a commercial product in 1996. In 2002, Tree Star released a Windows version. More information about the use and function of FlowJo is available at its website.