Basic animations can be generated through a Batch operation in the Layout Editor and played in a web browser.
Click the layout tab in the Layout Editor when you have the prototype layout setup to your satisfaction.
This will bring up the Create Batch Report dialog where you can select Web Animation (out of the drop down menu). Click the Create Batch Report button and an HTML movie will be generated with a frame for each sample in the current group.
FlowJo will attempt to open the animation in your default web browser. To open the Animation movie manually, locate the LayoutName.html file written to the specified Output file folder location and double click.
Layout Editor Web Animation batching will obey iteration settings. This means that they follow normal FlowJo batch operations and will only produce images for samples in the group being batched, one frame per sample. Web Animation movies will open in your default web browser.
Layout Editor animations are oriented towards visualizing trends across a group of samples as opposed to the Graph Window movies where the focus is on a single parameter in one file.
To learn more about making movies in the Graph Window, please see this page.