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.

All Files Pipeline

The All Files pipeline is created automatically. All FCS files that are opened are added to the pipeline. Applying operations to this pipeline will be added to all files.

Creating Pipelines

You can create new pipelines using the "Pipelines" tool in the left-hand tool panel. You will need to provide a name for the new pipeline.

Pipeline Filters

When a new pipeline is created you can add files manually to the pipeline or you can set a rule to automatically include files in the pipeline. By default you must add files manually. To auto include files, set the "Auto Include" switch to on. Then you will be able to add a condition to filter file names through to determine if they belong in the pipeline or not.

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 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 Pipelines

There are two different modes for viewing pipelines. These options are available by right-clicking on a pipeline:

By default, when you left-click on a pipeline it shows them as overlays

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 Export, 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.

Pipeline Templates

Often the same analysis is repeated over and over again for different experiments. To save time having to redraw all gates, switch transforms, and add statistics, you can create a pipeline template. This will create a template file that you can apply to future experiments. Once you have your pipeline set up, go to File->Save Pipeline Template. We doing the analysis for a future experiment, you can open the pipeline.xml file and your pipeline will be reconstructed and applied to your new FCS files.