Pipelines allow you to apply operations i.e gates, statistics, etc, to a group of files simultaneously. They also allow you to easily view overlays and batch export images of any population in the pipeline. Currently, there is only a single pipeline, All Files, which automatically applies to every file you open.

Adding Operations To A Pipeline

You add operations to a pipeline by dragging and dropping them from a population in the file tree to desired location in the pipeline hierarchy. When you drag a gate from a population to a All Files pipeline, the gate is applied to every file in the file tree. If desired, these gates can be independently adjusted per population by manually editing them one by one. You can also add statistics, cell cycle, etc by dragging and dropping them onto the pipeline hierarchy.

Viewing Overlays

You can easily view an overlay of a specific gate in the pipeline by selecting the gate in the pipeline hierarchy.

Batch Image Exporting

You can export images for a particular gate of a pipeline for each file in the pipeline. To do this, select the gate that you want to export in any file that is part of the pipeline. Then go to File -> Save Image and select the Batch Pipeline option. Now when you click Apply, it will save an image of the selected gate for each file in the pipeline and save them to your computer as a ZIP file.