Welcome! New to Cytoflow? Start with a screencast.

Are you on MacOS? A recent update has broken Cytoflow on MacOS. You can get experimental packages that should fix the problem here

What’s wrong with other packages?

Packages such as FACSDiva and FlowJo are focused on primarily on identifying and counting subpopulations of cells. While this is important for many different applications, it reflects flow cytometry’s origins in separating mixtures of cells based on differential staining of their cell surface markers.

Recent experiments in our lab and others have been more interested in using a cytometer to compare distributions of cells, asking how these distributions change in response to experimental variables. Existing packages don’t handle this gracefully!

How is Cytoflow different?

Note: this is still beta software! Caveat emptor!


There isn’t any! The binaries at the top of the page are all you need. On a Mac, you’ll have to extract the ZIP archive – then, just double-click to start the program! It takes a minute to decompress the one-click archive before it runs, though, so be patient.


The developer documentation is quite complete, but the GUI documentation is lagging. A good introduction is the screencast on Youtube. NOTE: This screencast is for an older version. Several new screencasts will be along shortly.

Help! I found a bug!

First, are you using the current version? To check, which version you’re using, go to the Help menu (Windows) or Cytoflow menu (Mac) and choose “About Cytoflow…”.

You can also try to reproduce the bug in the latest build from git HEAD. Those binaries are on BinTray.

If you have found a bug in the most recent version, there are three ways to report it. First, you can navigate to the Help menu and choose “Report a problem…”. This will open an email to the developers, including some information about the version of cytoflow you’re using and some logs.

Second, you can join the cytoflow-dev mailing list and communicate your bug to the developers directly.

Finally, you can submit your bug report to the Github issues tracker.

I want to keep up with new Cytoflow releases!

Great! Subscribe to cytoflow-announce and we’ll send you an email when a new version is released.

Are there screenshots?

There are screenshots.