Cytobank stores two principle versions of your gates. One version is what you see at any given time in the gating interface. These are termed Scratch Gates. The second version of your gates are what the rest of your experiment is working off of at any given time. These are termed Experiment Gates. These gates are used for statistics, illustrations, SPADE, viSNE, and everything that is not in the gating interface.
The "apply" and "apply and return" buttons
When actions are taken in the gating interface, differences accumulate between the Scratch Gates and the Experiment Gates. These differences could be small, as in the case of simply nudging a gate, or they can be large, as in the case of a long session of gating. The apply button sets the Experiment Gates to the state of the Scratch Gates. Put another way, it applies changes made in the gating interface to the rest of the Experiment. The apply and return button does the same thing but also returns you to the illustration, or in some cases, whichever screen you were on previously.
A common point of confusion is when gates are missing from certain parts of the Experiment but present in the gating interface. This can manifest as missing gates in the illustration, export statistics interface, viSNE, SPADE, etc. To avoid this problem, press the apply button when changes have been made in the gating interface such that they are applied to the rest of the Experiment.
Gating changes are saved continuously, not with the apply button
When gating in the gating interface, every action taken is saved immediately and overwrites the Scratch Gates. You can see this reflected in the status indicator that appears below the gating plot. No action needs to be taken on your part to save your gates. Your computer could crash one second after moving a gate, and you won't lose any work! Changes are saved continuously to the Cytobank cloud. The apply buttons simply apply the state of the gating interface to the rest of the Experiment as detailed above.
Gate versioning system
This article details the difference between Scratch Gates and Experiment Gates. To the end-user, only these two sets of gates are apparent. Behind the scenes, however, the functionality of the apply button is actually to increment and write a new version of the Experiment Gates each time the button is pressed. Each complete version of the collection of gates is saved in the Experiment. Currently, these versions are not accessible via the Cytobank interface. Only the latest version at any given time is used as the Experiment Gates for functionality within Cytobank. The one exception to this is via using the statistics endpoints of the Cytobank API. Get in touch with Cytobank Support if access to the gate versioning system would help your workflow.
Review of key points:
- It is not necessary to repeatedly press the apply button to save your work. It gets saved continuously!
- Press one of the apply buttons after making changes in the gating interface that you want to be applied to the rest of the Experiment.