Welcome! New to Cytoflow? Start with a tutorial.

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?



You can find the developer documentation at ReadTheDocs.. GUI documentation for the currently selected operation or view appears in the “Help” panel in the GUI. If you don’t see a “Help” panel, make sure it’s activated by going to the “View” menu and selecting “Help”.

Example Data

The Jupyter notebooks and screencasts use two example data sets.
If you’d like to play with them yourself, you can download them here:

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…”.

If you have found a bug in the most recent version, you can submit your bug report to the Github issues tracker.

I want to keep up with new Cytoflow releases!

Great! At the Github page, pull down the “Watch” menu and select “Releases only.”

Are there screenshots?

There are (slightly outdated) screenshots.