Note that you can manually type in the boundaries of a gate if you wish; you can specify the gate boundaries in terms of channel number, absolute fluorescence, or percentile within the subset:

you can bring up this dialog by selecting "Manually Enter Gate" from the "Graph" menu in the Graph window.

Or you can create gates by using one of the gate tools in the graph window:

from left to right: point tool, rectangular gate tool, 1D gate, quadrant gate, ellipse.

Gate tools are shown in the floating graph tools window, and include a range tool (for histogram plots), as well as 2D tools such as rectangles, polygons, ellipses, and quadrants. The selection tool (arrow) is used to select gates before moving them, deleting them, or modifying them. Selected gates are indicated with square "handles".

Depending on what you select in the preferences, FlowJo may automatically select a gating tool when you click in a graph window.  If your preference is to have FlowJo automatically select a gating tool, you can also choose to have the polygons or rectangles tool as you default for bivariate displays.

The first gate is a one-dimensional gate, consisting of an upper and lower bounds. It can only be drawn on a histogram or CDF plot. Simply point the cursor in the graph window where you wish to have the upper or lower bounds, click on the mouse, and while holding the mouse down, drag to the other extent of the gate. FlowJo draws a horizontal line in the graph to show you the bounds of the gate that you have selected. Later, you can click on the line to move it right or left (changing the bounds of the gate), or up or down (which does not change the gate itself). Alternatively, you can move the upper or lower bound to extend the gate.

The other four types of gates (rectangular, polygonal, quad or ellipse)are drawn on any bivariate plot (contour, density, zebra or dot plot). A polygonal gate with any number of vertices is started by clicking within the graph window. Move the cursor to the next vertex; click to generate another point in the polygon. You may close the polygon either by clicking on the originating point, or by double-clicking on the next-to-last point. (You can cancel the generation of a polygon by hitting the "spacebar" key on the keyboard at any time).

To draw a rectangular gate, select the appropriate tool. Hold the mouse key down as you drag to the opposite corner of the rectangle. Rectangular gates can be computed considerably faster than polygonal gates; you may wish to use them when you analyze large data files.

An ellipse gate can be created by selecting the ellipse tool. Ellipses can only be horizontally or vertically oriented. Click and drag the outline of the enclosing rectangle for the ellipse.

Use the quadrant tool to create four non-overlapping rectangular gates. For more information on creating and using quadrant gates, click here.

Once you have created a gate (except when you use the quadrant tool), FlowJo asks you to name it. FlowJo supplies a default name based on the parameters used to draw the gate; you may type in any name you wish. Note that gate names must be different than any other "sibling" of that gate; i.e., a population cannot have two gates with the same name (see information on naming subpopulations).

You can change a gate by moving it or moving one of its vertices; the gate is automatically recomputed as you change it. You can delete a gate by pressing the delete key when a gate is selected.