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 really 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: FlowSOM Clustering Algorithm and BD Index Sorting

FlowSOM: FlowSOM is a state of the art clustering and visualization technique, which analyzes flow or mass cytometry data using self-organizing maps. With two-level clustering and star charts, the algorithm helps to obtain a clear overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. The method has been implemented as an R/BioConductor library and published in Van Gassen et al., Cytometry A, 2015.
Beta release - tested with FlowJo v10.4.1.
BD Index Sorting: A robust tool for automatically gating wells in index sorted data from BD's cell sorters the FACSAria and FACSMelody.
Beta release - tested with FlowJo v10.4.1.

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 SeqGeq Plugins

Auto-Gate for Categorical Parameters: This tool allows users to automatically gate categorical parameters
Beta release - tested with SeqGeq v1.1.0 Preview.
Image credit: Creative Commons license.
Most Highly Expressed Genes: For researchers wishing to create a gene set and corresponding population, according to user input thresholds for both expression and top expressors.
Beta release - tested with SeqGeq v1.1.0 Preview.
Image credit: Creative Commons license.
Differential Gene Expression: Generate a gene set containing parameters expressed differentially in one population versus another, above a customizable threshold.
Beta release - tested with SeqGeq v1.1.0 Preview.
Image credit: Creative Commons license.
Seurat Pipeline: Utilize the whole Seurat pipeline developed by the Satija Lab in one easy to use plugin. Yielding tSNE parameters, KNN clustering, DE gene sets for each cluster, and QC all from one dialog. WARNING: May blow researcher's minds!
Beta release - tested with SeqGeq v1.1.0 Preview.
Image credit: Creative Commons license.

Available FlowJo Plugins

FlowAI: This tool allows users to clean their data using a new algorithm developed by Gianni Monaco et al. at the SIgN (A*STAR). FlowAI works by checking parameters over time and looking for deviations outside the statistical norm. FlowAI provides similar outputs as the FlowCLEAN tool, but with more sensitivity.
Beta release - tested with FlowJo v10.4.
Image credit: Hamish, The Noun Project, Creative Commons license.
Calibration: For researchers wishing to calibrate parameters using MESF beads, this tool will automatically detect peaks, and allow users to assign known molecular equivalents to those control peaks. The tool will then perform a linear regression between the observed peak fluorescence intensities and manufacturer provided molecular values, in order to generate a corresponding calibrated derived parameter.
Beta release - tested with FlowJo v10.4.
Image credit: Hamish, The Noun Project, Creative Commons license.
Virtual Reality: The Virtual Reality FlowJo Plugin attempts a linear regression and one-dimensional plotting within virtual reality based on a selected population and parameter data. Note: This is a third-party plugin. This plugin has had limited internal review by FlowJo, and support may be limited.
Image credit: Delwar Hossain, The Noun Project, Creative Commons license.
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 Amazon Web Services 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, updating your team regarding changes to the FlowJo workspace. A dialog box is presented upon each save, allowing you to specify recipients and an additional custom message.
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.
Beta release - tested with FlowJo v10.3.
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: Initializes a new project using a simple loop tool in JavaScript.
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.

Advanced Relative Gate: Creates a set of relative gates for multiple samples. Download the script now, or view the documentation.
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: 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 techsupport@flowjo.com.