Plugins are apps that extend functionality of the FlowJo application.  Plugins are free add-ons, hosted on the FlowJo Exchange.

A video demonstrating Plugin installation.

FlowJo has an open API that allows us, or anyone else, to rapidly develop cutting edge tools without modifying the entire FlowJo application.  Please visit the Exchange to peruse the current plugin offerings.  For help installing a plugin,  please see the Installing Plugins page for details.

Interested in writing your own FlowJo plugin?  We provide a plugin developer guide to help get you started. 

Within FlowJo, plugins and the Exchange can be accessed from the Workspace tab (by default), Population band, Plugin selection.


Two primary plugin types

There are two primary types of plugins, population plugins and workspace plugins. 
Population plugins work by selecting a population then starting the plugin by selecting it from the plugins dropdown menu.  Whatever actions the plugin specifies will be applied to that population.  Almost all of the plugins we offer are population plugins, so be sure to select a population to apply the action to.
Workspace plugins are added by selecting Add Workspace Plugin from the Plugins dropdown.  Most workspace plugins perform some action on Save, or data load.  One example is CytoNorm, which process a folder of data for loading into FlowJo. 

Getting Started Using Plugins

We recommend the Plugin Wizard as the first Plugin tool to install.

The Wizard is itself a plugin, so you will need to go the diagnostics tab of the FlowJo preferences and specify a folder for FlowJo to load plugins from, download the Wizard and add the jar file into the folder you specified, as described on the How to Install a Plugin page. 

Plugins load when FlowJo is started, so if you have FlowJo running when you add a new plugin to the folder you have specified, you will need to restart the program to refresh the list.   Once started, select a data file since the Wizard is a population plugin that needs a population to be selected, then choose the Wizard from the plugin menu. 

Many plugins create derivative files such as graphs, reports, or action logs, so FlowJo requires that you have saved your workspace prior to running a plugin to ensure that workspace has a unique name, and then creates a folder with the same name as the workspace where all outputs are placed.  If you have not saved, you will see a prompt to save when you start the first plugin.

The Wizard will bring up an interface with five steps for setting up and maintaining plugins:

  1. A link to download R for plugins that are R-dependent.
  2. A place to set the R path, so FlowJo can find R on your computer.  This path should point to the actual R application, generally in the bin folder.
  3. A checkbox to auto-install R libraries and packages required by R dependent plugins. 
  4. A place to set your plugin folder path.  If you are running the plugin Wizard you will have already done this, so it’s only useful if you intend to change it.
  5. A tool that checks to see what version of each plugin you have, that provides links to the exchange to download any plugins for which an update exists.


How-to documentation for specific plugins

  • The card for each plugin on the Exchange contains a summary of the plugin and a link to the publication if it has been published.
  • Each plugin download comes with a How-to document.
  • Many plugins have detailed movies on our plugin demonstration page.
  • There are many webinars that use plugins, and a webinar for each suite of plugins on our recorded webinar page.