Welcome! New to Cytoflow? Start with a screencast.
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?
An emphasis on metadata. Cytoflow assumes that you are measuring fluorescence on several samples that were treated differently: either they were collected at different times, treated with varying levels of inducers, etc. You specify the conditions for each sample up front, then use those conditions to control the analysis.
Cytometry analysis represented as a workflow. Operations such as gating and compensation are applied sequentially; a workflow can be saved and re-used, or shared with your coworkers.
Easy to use. Sane defaults; good documentation; focused on doing one thing and doing it well.
Good visualization. I don’t know about you, but I’m getting really tired of FACSDiva plots.
The point-and-click interface is built on Python modules. Do you analyze data with Python? If so, head over to the developer documentation to use these modules in your own workflow. They have been designed to work well in a Jupyter notebook; in fact, the GUI will even export a workflow directly to a notebook!
Free and open-source. Download the source code from the GitHub project page and modify it to suit your own needs, then contribute your changes back so the rest of the community can benefit from them.
Note: this is still beta software!
It is stable and full-featured, but you may still encounter bugs!
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.
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”.
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…”.
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.