FCS Express: Gates

To analyze cell sub populations, you create gates and apply those gates using one of many methods. In FCS Express, plots and statistics update immediately in real time as you move gates, markers, or quadrants, allowing you to evaluate your gate placement on the go.

FCS Express supports five types of drawing gates, and another type, called combination gates, which can combine any number of other gates in several ways. You can also create gates directly on images with FCS Express Image Cytometry.You can create an unlimited numbers of gates or create a gate matrix.

Learn more about gates in FCS Express with the links and videos below:

Gating types available in FCS Express 6
Rectangular Gates: Gates that are in a square shape. Elliptical Gates: Gates that are in an elliptical shape Polygonal Gates: Gates that are in the shape of a polygon which are defined by several vertices and straight lines connecting the vertices.
Freeform Gates: Gates that are drawn in an arbitrary shape. The gate boundaries can be curved. 1D Gates: Gates that exist only in one dimension. Well Gating on Heat Maps: Gates that are applied to one or many wells on a heat map plot.

Well Gating only available with high content add-on.

Applying A Gate

FCS Express makes it easy to to apply a gate (ie. restrict the cells which appear on a plot to the cells that pass through a specific gate).  View the short videos below for examples of:

  • Applying a gate from the gating toolbar
  • Dragging and dropping a gate to create a new plot
  • Dragging gates from the gate navigator to a plot
Applying a gate using the gating toolbar

Dragging and Dropping Gates

Data Specific Gates

FCS Express allow you the ability to assign gates to specific data files that have been loaded in the data list. When a gate is converted to a Data Specific Gate for a given file, the shape and position can be modified for the specific file independently from other data files. When using the Data Specific Gate feature, the different gating positions and shapes between data files are then stored and automatically used when displaying plots or making calculations

Learn more about using Data Specific Gates.

Emphasizing Gated Populations

Gated populations can be emphasized on dot plots either arbitrarily or by a low-frequency threshold, drawing attention to subsets of interest. In the example below, the low-frequency population in the green gate has been emphasized.

For a brief tutorial on how to enable this option, please click here.

Hierarchical Gating

FCS Express supports hierarchical gating to create gates based on subsets of other gates. In the example below a "Cell" gate was created with subgates created for CD3 and CD19 positive cells. A further hierarchy was created for those cells in CD3 that are also CD8 positive.

Gating logic is flexible and may be adjusted at any time. Gates may also be created hierarchically by default by adjusting your preferences.

Flexible gating formulas

For more sophisticated gating, you need to combine more than one gate into a formula. To create the formula, simply open a Gate View window, right-click, and select Add Combination gate.  You will then be able to use boolean expressions to create powerful new gates.  Below is an example of using combination gates to include cells in Gate 1 and Gate 2, Gate 1 or in Gate 2, and lastly excluding those cells in Gate 1 and Gate 2.

Right clicking on the Gate View window will allow you to Add a Combination Gate.