Analysis Software


FluoroFinder’s panel builder tool is the obvious choice to simplify your flow cytometry experiment design, but you will also need to choose software for efficient data analysis.

Your lab or core facility may already have one or more analysis software packages installed into their flow cytometry workflow. However, not all software is created equally. If you do find yourself unsure of which option is best suited to your needs, there are many factors to consider.

Here we outline some of the most important considerations when choosing a flow cytometry analysis software.

  1. Budget – There are many open-source (free) analysis software options created by academic labs or collaboration groups. While commercially available software will often have cleaner user interfaces and more convenient functionality, you may find free tools that can perform the necessary analysis just as well. See lists of our favorite open source and licensed analysis software options here.
  2. Specialization – Certain types of flow cytometry experiments, such as imaging cytometry and single-cell analysis, will require specialized analysis software. For example, Astrolabe offers users the ability to gain rapid insight into single-cell data
  3. File compatibility – Be sure to consider which file types, acquisition software packages, or cytometers the analysis software can support. Not all options may be compatible with your data.
  4. User interface – Flow cytometry data analysis can be intimidating, especially for new users. Many software options offer intuitive interface design and drag-and-drop functionality, walk-through tutorials to minimize confusion, and machine-learning algorithms to automate some decisions.
  5. Data visualization/presentation – Consider how you plan to present your data. Many analysis programs can display data in dot plots, histograms, or 3D plots with options to export/print publication-quality graphics.
  6. Data sharing – Are you working with researchers in different locations? Some modern analysis software allows researchers to analyze, manage and store their data in the cloud for simplified collaboration.
  7. Reputation – Always consult with colleagues and other researchers for their recommendations before committing to a software selection.


In conclusion, there are many things to consider when selecting a data analysis software. We hope this list of considerations and our list of flow cytometry software options help when selecting the best option for your experiment.