Data transformations allow you to create custom parameters through various algorithms in FCS Express as well as integrate directly with R or Python.  The Transformations navigator is an intuitive dialog and makes it easy to apply your transformations to plots via a quick drag-and-drop.  Simply click on the Tools tab→Transformations to launch the Transformations navigator. FCS Express does not require R/Python scripting or programming for any algorithms available in the software. However, if you prefer to use R/Python, or desire to use your own custom scripts, the easy to use Transformations interface supports direct integration with R/Python.

All transformations can be applied to both Flow and Image cytometry data sets.

Available Algorithms and Tools


Please visit our extensive resources on data transformations via the quick links below so you can get up and running today.

Quick Examples

Pipelines in FCS Express are a set of data processing steps that stand alone or are connected in series.  The output of a step can be applied to a data file or utilized as the input of the next step, or series of steps, that may be applied to your data. No plugins, no programming, just results!

The vast majority of commonly used algorithms for data analysis are actually pipelines, with tSNE (and its variants) and SPADE being two examples. However, when those algorithms are implemented as a one calculation, user customizations are limited to the what the specific implementation allows. Pipelines in FCS Express increase the computational flexibility and granularity of running algorithms and data transformations while giving users the unique ability to create their own transformations.

FCS Express provides a wide variety of pipeline steps for you to choose from. See our full list of all available steps and contact us if there are steps you are interested incorporating into FCS Express that are not yet available.

Feature Support

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Manual and Tutorials

Transformations in the FCS Express Manual

Video Resources

On demand video content