Each instrument in our facility is connected to a computer and data is acquired in specific software. While FACSCalibur uses Cell Quest, Fortessa and Fortessa X-20 use FACS DiVa. For flow cytometry data analysis, we recommend the use of FlowJo. Information about these software below.

Note that instructions on how to use the software associated with the analysers can be found in a guide next to the instrument. Feel free to contact the FCF staff for assistance or advice regarding your data acquisition and analysis.


FlowJo is a flow cytometry data analysis software that provides an easy-to-use analysis environment. The FlowJo can be used for immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, or plate screening assays to name a few.

Where can I use it? This software is installed in our 2 analysis workstations or, upon request, a software licence for a lab computer can be arranged.

How can I learn how to use it? You can send an e-mail to the FCF staff to schedule a 2-hour FlowJo training or to ask for advice regarding FlowJo tools or how to visualize your data.

You may find more help in the following sites:

  1. FlowJo Website
  2. FlowJo University or FlowJo Tutorials
  3. FlowJo blog


BD CellQuest Pro software can be used for data acquisition in FACSCalibur and offline data analysis. This software distinguishes between an experiment document and a data file. The experiment document contains elements such as plots, regions, gates, statistics, markers, and annotated text. Data files are not saved in the Experiment document, but rather the software saves a reference to the data files that contain the information needed to recreate the plots and stats on the Experiment document.

Download a short user guide or a long user guide for guidance. You can also find a guide with the steps to follow to create an experiment and acquire data here.


BD FACSDiva software is a data acquisition and analysis package used in BD LSR Fortessa and BD LSR Fortessa X-20. The software also provides interesting analysis tools such as experiment templates, automated compensation calculation, hierarchical gating, the ability to copy and paste gates, and biexponential display. BD FACSDiva software uses a Browser view that allows its users to easily organize experiments, group specimensand tubes, design global or tube-specific analyses, and set independent cytometer settings.

Download a quick user guide or a long user guide.


Flowing is a free data analysis software for Windows. Its real strength is in high throughput data analysis. "I need statistics, dot plot images as 96-well layout and overlay histograms. Oh, and the number of samples will be about 20000, so analysis should be performed automatically". Flowing software package solves the challenges of the automation of the analysis, still remaining so easy to use. No coding, no complicated interfaces.

More information here.

CytoFlow (Python package with UI)

CytoFlow is a free Python package for quantitative analysis of flow cytometry data. Cytoflow includes low-level modules that programmers can use to manipulate, analyze and visualize cytometry data, as well as a graphical user interface that lets non-programmers perform analyses and share workflows with colleagues.

More information here.

FlowCytometryTools (Python package)

FlowCytometryTools is a free Python package for visualization and analysis of high-throughput flow cytometry data. It creates flexible and scalable analysis while providing a simple programmatic interface to work with flow cytometry data. The package is specifically tailored for high-throughput analysis. It provides an interface that can directly work with collections of flow cytometry measurements (e.g., 96-well plates). Basic familiarity with the python programming languages is recommended.

More information here.