The Graph Window is the analysis interface that facilitates data visualization and gating. FlowJo’s Gating tools are powerful instruments that help you get the most out of your FACS data. 

Gating Defined

Gating refers to the process of selecting a subset of the collected events for further analysis. Subsets can continue to be gated to generate further subsets, until a collection has only the cells for which a graphic display or analysed statistics are desired.

Once a gate is created with a gating tool, double clicking on the gate will open a new Graph Window displaying the selected population. This population is often referred to as the child gate, and the population that created it is called the parent gate. In the figure below a polygon tool was used to draw a star- shaped parent gate (left). The child gate on the right only contains the population of cells contained within the parent gate.


The process of gating simply creates a new population. Naming subpopulations is important. Siblings (subsets from the same parent but displaying different parameters) with the same names are not allowed to avoid confusion.  In general, avoid using duplicate names of subpopulations within any given sample.

Gating Menu

FlowJo X has a variety of gating options available in the graph window interface. Gating options are located above the graph and are shown in the screenshot below.

The gating tools are as follows:

Arrow tool – Used to select objects

Rectangle gates – Rectangular gates are the most efficient to calculate, making this a primary tool for rough gating.

Quad gates – Four rectangular gates sharing a common center point, used to divide non-overlapping populations.

Ellipse gates – This is the tool to draw round  gates over a region of interest.

Polygon gates – Create a polygon gate by clicking to make new vertexes. Double click to complete.

Pencil gates – Create a polygon gate drawing a region of interest.

Autogates – Create a polygon matching the distribution of events in the two specified dimensions.

Curly Quad gates – Quad gates, but with exponential curves in each dimension to better model increases in the data.

Spider gates – Spider gates are abutting polygons that share common vertexes.

There are also ranged gates and the bisector tool which are only available for use with univariate plots (histograms, CDF), shown below.

B3 .fcs_ Ungated - FlowJo-5

You can read more about gating at the links below.

Drawing Gates

Editing Gates

Naming Gates

Manual Gates

Magnetic Gates