FlowJo Exchange

Unleash your analysis using FlowJo™ as a platform.

Welcome to the Exchange

The FlowJo Exchange is a repository maintained by FlowJo, LLC that allows users to upload annotated scripts and download shared scripts. Plugins are a new addition to the Exchange that allow users to create their own extended functionality for the FlowJo application. The open plugin architecture introduced with 10.1r7 allows FlowJo users access to cutting-edge tools that can be integrated into their current FlowJo analysis workflows, so any tool can be integrated into FlowJo.

Don't worry, we are pretty obsessive about documentation. Each script, plugin, or visualization we provide includes instructions that step you through how to use it, and we urge others who post to do the same. No JavaScript, HTML, or black belt skills are required.

Featured: Cell Ontology Plugin

The Cell Ontology plugin queries a cell ontology database and matches the cell or population in your FlowJo workspace to specific cell types. Almost all applications in flow cytometry rely on phenotype markers, and the CellOntology database maintains a record of published definitions of cell types with a myriad of phenotypic markers and their associated functions, etiologies, or biological contexts.

This plugin retrieves suggested nomenclature based on a ranking score, creating a single CSV file containing suggested names and a cladogram detailing your cells' relationship to other known cell types. Note: This plugin uses the flowCL package within an R statistical computing environment.

This is a new version of this plugin, and is recommended for users of FlowJo 10.2 or later.

Download the plugin now
View the plugin documentation

Tool types

There are four types of tools here, which can all be used with FlowJo:

  1. Plugins
  2. Scripts
  3. Visualizations
  4. Shipped Plugins

1. Plugins (NEW)

Yeah, we can cluster that. If you have an algorithm or application that needs to do something upon opening or saving, or you would like exported population data and user-specified parameters passed to your application, we can do that. In fact, we can bring the clusters back into FlowJo so everyone can use what you have written. To learn more, please see our FlowJo for Developers page (coming soon).

Note: You must be running FlowJo version 10.1r7 or higher to use plugins. Earlier versions do not support plugins.

Example Plugins

See these examples for plugin development and documentation done well.

How to Install FlowJo Plugins

The plugin should now be ready for use. You access most plugins from the Workspace ribbon, Populations band, Plugins task. See the User Guide section of the plugin’s documentation for instructions on how to use the newly-installed plugin.

Available Plugins

Auto-Gating: Allows FlowJo users to make distinct gates around their samples based on child-parent percentages. This plugin generates an optimal sub-population that matches a user's specified percentage.
Image credit: Alfredo Hernandez, The Noun Project, Creative Commons license.
AWS-S3: Uploads FlowJo workspace files to an AWS S3 server. Using the AWS S3 service with FlowJo gives you the ability to upload and download workspaces as a remote backup or share workspace environments with others. The user attaches his or her workspace to a specific S3 bucket, and the workspace is uploaded to this bucket when the workspace is saved.
Image credit: ProSymbols, The Noun Project, Creative Commons license.
Email Notification: Sends auto-generated email notifications when a FlowJo client workspace is saved. This communication promotes changes to the FlowJo workspace. Email notifications may be sent to recipients when the FlowJo workspace is saved in the FlowJo client.
Image credit: Jim Slatton, The Noun Project, Creative Commons license.
FlowClean: Automatically identifies and flags fluorescence anomalies in flow cytometry data so that these can be easily removed. This algorithm uses the R statistical computing environment.
Image credit: Julieta Felix, The Noun Project, Creative Commons license.
LIMS Integrator: Provides PostgreSQL integration with FlowJo for lab management purposes. This plugin allows for the integration of user information associated with a FlowJo workspace and a PostgreSQL database. Except for the initial setup of a PostgreSQL server, all other setup is handled through the plugin, such as database and table creation.
Image credit: Alfredo Hernandez, The Noun Project, Creative Commons license.
OPTICS: Allows users to perform density-based reordering and cluster detection on populations within FlowJo. This population plugin performs density-based reordering and cluster detection to extract the clusters present in a population node. The user can select what parameters they wish to cluster the data on.
Image credit: Delwar Hossain, The Noun Project, Creative Commons license.

2. Scripts

FlowJo's Script Editor is integrated directly into the core of FlowJo, and gives real-time access to statistics, gates, groups, and metadata to create custom analysis tools within FlowJo. This access makes it easy for:

Scripts produced in the Script Editor can be saved as text files, shared, and run by anyone in three clicks by loading them into a FlowJo workspace and clicking Run.

Available Scripts

Indexed Sorting: Compiles index sorting keywords and creates a gate for each cell, with the well location as the name.
Image credit: Hans Paul Mösl Junior, The Noun Project, Creative Commons license.

Basic Loop: Basic loop tool in JavaScript to initialize a new project from.
Image credit: Rflor, The Noun Project, Creative Commons license.

Collection Order Sort: Creates a sortable keyword based on day-month-year metadata.
Image credit: Demograph, The Noun Project, Creative Commons license.

Control Based Inclusion Gating: Automatically creates "positive gates" using control samples' properties.
Image credit: The Noun Project, Creative Commons license.

Relative Gate: Creates a gate relative to a pre-defined (negative) population.
Image credit: Rflor, The Noun Project, Creative Commons license.

3. Visualizations

Some of us spend our weekend playing with visualizations (yes, seriously), and we'll post some here with some instructions for use.

4. Shipped Plugins

The plugins listed below are included with FlowJo v10.1r7 and later. We include them here in case you need to update or re-install them. They can be installed in the same manner as any other plugin—see How to Install FlowJo Plugins above or our plugin documentation for details.


Cell Ontology: New Version! Determines the name and etiology of a gated cell or population by querying a published set of cell type definitions. This plugin uses the R statistical computing environment.
Image credit: Icon Mafia, The Noun Project, Creative Commons license.

DownSample: Creates a new gate containing a specified subset of data points or events, which can be used like any other gated subset or population node within FlowJo.
Image credit: Creative Stall, The Noun Project, Creative Commons license.

FlowMeans: Automatically identifies cell populations in flow cytometry data using K-means clustering.
Image credit: Thomas Helbig, The Noun Project, Creative Commons license.

SPADE: Visualizes mass cytometry data, creating a network graph file (GML), PDF output, and adding a "cluster" column to FCS files.
Image credit: Ecem Afacan, The Noun Project, Creative Commons license.

t-SNE: Visualizes reduced data dimensions while still maintaining the structure of the data.
Image credit: Paul Stevens, The Noun Project, Creative Commons license.

Need to cite the Exchange?

If you use these tools in your research, please give credit as follows:

J. Quinn, S. Duncan, M. Golden, M. Swindle, S. Weiss, M. Stadnisky. FlowJo Exchange : A means of meeting the computational needs of the flow community. CYTO 2015: XXX Congress of the International Society for the Advancement of Cytometry. Glasgow, Scotland. June 2015.

...and please be sure to let people know what script you used.

Need Help?

Drop us a line at exchange@flowjo.com or techsupport@flowjo.com.