Drawing Gates to Identify Cell Populations
You can also view videos of how gates are drawn on our tutorial pages:
Read a definition of gates in flow cytometry on Wikipedia.
Note that if your experiment was part of a kit, such as the T-cell kit, gates will be drawn automatically for you. You can still follow this protocol to check and edit the gates.
1. Open a working illustration for the experiment you want to gate.
2. Open gating by clicking on “Edit” within the Populations box at the top of the page.
For some new experiments, the Populations box should display text indicating that you need to draw gates. If gates have already been drawn (e.g. with kit experiments), then you will see a list of populations and the “Edit” button will be available. Click whichever of these two buttons is available to open the gating interface.
A gating program will load within the page. You need to have Java installed to use this program. (See System requirements for details)
3. To draw a new gate and define a population, click on the Polygon gating tool at the top of the gating program. Then click a series of points to draw a polygon. When you close the shape (either by clicking back on the first point or by double-clicking on the last point of the drawing, which will draw a line to connect to the first point), a dialog box will ask you to name the gate.
4. Double-click on the gate to make it the active population.
Note that the active population changes in the drop-down menu as you drill into each new population you create. This creates a tree of gates, which you can navigate “up” and “down” using these buttons at the top of the gating program.
5. If you want to check whether a gate “fits” all the files, click the “Check Gate” button. This will open a view of this gate across all the files where it exists.
It is possible to create Stand Alone Gates in Cytobank, where a gate is one entity but has a different shape on each file. To do this, simply toggle the gate type to “Stand Alone” from the default of “Global”. Global gates are the same on all files. We recommend using global gates whenever possible.
6. You can add a subgate to the active population, or you can set the active population back to "Ungated" to create a new population. You can change the X and Y axes without changing the active population.
7. View a tree of the populations by clicking “View Populations” at the lower left.
8. When you are done gating, return to the illustration page by clicking “Save and Return to Illustration”.
Gates and populations are automatically saved, although if you close the browser window the last action you took may not be saved.
