The Cytobank platform has comprehensive gating tools for data analysis. Here, we will give an overview of gating and gating-based visualization in the Cytobank platform. Please see The Difference Between a Gate and a Population to learn more about how to create populations using gates.
In the Gating interface anatomy section, you can click on each item to go to the dedicated support article about the gating tools to help you navigate.
Video overview
For a complete overview of gating in the Cytobank platform, see our video below!
Navigating to the Gating Editor
From within an experiment, click on Gates>Gating Editor in the experiment navigation bar.
The Gating Editor is where you can create gates and populations and visualize them. In the Gating hierarchy you can view the gating hierarchy by files and population.
Gating interface anatomy
Gating interface anatomy
Please click on the highlighted text to learn more in the dedicated support article about all the gating tools.
(1) Undo/Redo
To go back to previous state or re-do an action on the gating page.
(2) Gating tools
To choose between Rectangle, Ellipse, Polygon, Quadrant, Split and Range gate tools to draw gates around cell populations.
(3) Load gates
To import gates to the current experiment from another experiment or by uploading gating-ML. Under this menu there is also the option to save a gate version or load a previously saved one.
(4) Cluster gates
To create cluster gates with cluster channels.
(5) Reset all
To remove all gates and populations from the gating interface. Reset all doesn’t remove any existing gating group.
(6) Compensation
To choose the compensation.
(7) Gates:
It shows a list of the gates created. Gates are the coordinates of the X and Y channels and do not carry hierarchical information. Gates can be used to build hierarchy to define a population.
When gating groups are enabled, the list displays the gating group names and the gates that belong to each group. Each gating group can be collapsed by clicking on the arrow displayed at the left side of the group name.
(8) Syncing File/Pop
These columns indicate the syncing status of each gate across files and populations. Read this article to learn more about all the possible combinations.
Clicking on this link will bring you to the Sample Tag Manager page, where the gating groups dimension can be enabled and files can be assigned to different gating groups, to allow for the definition of unique gating strategies for each group of samples.
(10) Population:
It shows the current active population displayed in the plot. The up and down arrows to the right can be used to move up or down the population list.
(11) File:
To show the current active file displayed in the plot. The left and right arrows to the right can be used to move up or down the file list. Click on the sample tag icon next to the search bar to select which experimental dimensions to show in line with the file name. If gating groups are enabled, the dropdown will show the possibility to display gating group names.
(12) Plot settings:
To change the plot settings.
Click on the setting icon to show the Plot setting window. Please see the link for more information on the Colored by Channel feature.
(13) Population tree:
List view of population hierarchy. If the experiment includes gating groups, one population tree per gating group appears. Click on the arrow near the gating group name to collapse/display the population tree.
(14) Boolean expressions:
To view and create populations by Boolean expression.
(15) Sunburst view:
Sunburst view of the population hierarchy.
For Research Use Only. Not for use in diagnostic procedures.