How to create gates and populations

Table of contents

Click the links below to jump to the relevant section.

  1. Background: The difference between gates and populations
  2. How to create gates and populations
  3. How to rename/delete gates or populations
  4. The impact of deleting gates or populations


The difference between gates and populations

In the Cytobank platform, the terms population and gate are different, and the distinction is important to understand.

A gate is a shape drawn on a plot to encapsulate a set of events. It reflects the coordinates of the X and Y channels. It does not carry any other information such as hierarchy or complex cellular identity. For example, if you draw a CD4+ gate on a CD4 vs CD8 plot, that CD4+ gate corresponds to the coordinates of the CD4 and CD8 channel and does not define CD4+ T cells. To define the CD4+ T cells, we will need additional gates like CD3+ to define the hierarchical order by Boolean expressions. 

To build information about hierarchy and to categorize cellular identity from gates, populations are used. A population is simply a collection of gates with certain Boolean expressions. In the example above, the population CD4+ T cells could be defined by the gates Scatter AND Live cells AND singlets AND CD3+ AND CD4+. This is the gate set of the population, and after applying all the gates, you will have the events of interest that define the actual biological population of interest.  Since gates and populations are decoupled, it is important to understand how to create populations using gates and Boolean expressions.


How to create gates and populations

Gates can be created using the gating tools in the Gating Editor. The gates are listed without hierarchy, whereas the populations are listed in hierarchical relationships, with statistics in line.  During the gating process, you can do sequential gating to create populations. For example, you can complete the gate on CD3+ and then create a CD4+ gate under CD3+. This can be done either by double clicking on the gate in the plot or choosing the corresponding population from the drop-down menu in the Population selection box.  Populations can also be created using the Boolean expression builder under the Boolean expression tab. 


The created gates will show on the left side of the plot. The corresponding populations will show the proper hierarchy order on the right side of the plot in the Population tree tab. 

Population tree

The population tree shows the populations with hierarchical order, each population is nested under the proper parents. It shows the gate name, percent of parent and the event number. You can also click on the population to select it. There will be menu options that appear to allow you to Unselect, Prefix, Suffix, Copy and Delete. Please see this article for details on Population tree.

How to rename/delete gates or populations 

To rename the gates or population, just mouse over the gate or population in the Gates or Population tree and click on Edit to rename. Please note that the Gates name and population name are independent of each other. If one changes, then the other won’t automatically change. Deletion can be done the same way. 

In the Population tree, you can also select multiple populations to perform change of Prefix, Suffix, Copy and Delete with all the populations selected. 


The impact of deleting gates or populations

Gates and populations are different in the Cytobank platform. Deleting gates and populations can have different impacts depending on the Boolean expressions they are in. 

When deleting gates, it is important to pay attention to where those gates have been used, as this might affect the corresponding populations.

  • If a gate was used to define only one population, deleting the gate will also result in deleting the corresponding population.
  • If a gate was used to define several populations using the AND operator, deleting the gate will NOT delete its correlated populations but those will now have a different hierarchical order and, therefore, no longer be the same populations you created before. Please double-check if you do need to delete gates to make sure no population will be affected by this.
  • If a gate was used to define one or several populations using an operator other than AND, it must be removed from other expressions prior to being able to delete it.

When deleting populations, similar scenarios apply:

  • If the populations are part of Boolean expressions that involve ONLY AND expressions, they will be deleted upon your confirmation. Please double check the gating hierarchy to make sure this is what you intended to do. 
  • If the population is part of Boolean expressions that involve other than AND, it must be removed from other expressions prior to being able to be deleted. 

*For Research Use Only. Not for use in diagnostic procedures.

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