FCSalyzer: flow cytometry analysis

I came across a free, cross-platform, flow cytometry analysis program, called FCSalyzer. Its author is Dr. Sven Mostböck and the program is under active development. I gave it a try and I should say, it is really promising. Although still in alpha stage of development, it provides all the basic functionality one would expect from a flow cytometry analysis software.

I made a SlackBuild for FCSalyzer and submitted it to SBo. A complete list of supported file formats can be found in /usr/doc/FCSalyzer-0.9.12_alpha/Datafiles.txt. I have used it to analyse data files acquired by Fortessa and Calibur. The program is quite stable and among its current features are:

  • dot and density plots
  • histograms
  • creating regions and gates
  • statistics, with the option to export them as a text file
  • quadrants and markers
  • overlays
  • …and more!

The program provides useful and intuitive keyboard shortcuts for its key operations, such as:

  • Ctrl + D to duplicate a histogram or dor plot
  • Ctrl + F for formatting
  • Ctrl + Page Down to switch to next data file
  • Ctrl + Page Up to switch to previous data file
  • Ctrl + T to bring up statistics

Here’s an example of my own data, showing density dot plots, gating, histograms, statistics and overlay:


3 Comments on “FCSalyzer: flow cytometry analysis”

  1. […] decided to make a ratiometric flow cytoetry analysis in FCSalyzer, since the program is free, cross-platform and easy to use (also, I just like it a lot). Such […]

  2. Nagarjuna says:

    i used it today for some basic analysis of data files that wouldn’t open on any of the other free softwares

    very easy to use – big thank you to the creator of the software and for sharing it for free

    i will try out regios/gates/compensation later and update my feedback

  3. slackalaxy says:

    I am sure Dr. Mostböck will be happy to hear your feedback, as well. Here’s a discussion about the program on SourceForge:


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