In order to use Python to analyze, perform machine learning on, or plot flow cytometry data, you can read FCS data files into dataframes using the FCSparser package.

The data in our demonstration were originally from:

Xiong, L. L., Garrett, M. A., Buss, M. T., Kornfield, J. A., and Shapiro, M. G. (2022). Tunable temperature-sensitive transcriptional activation based on Lambda repressor. ACS Synthetic Biology, 11(7).

We demonstrate how to use FCSparser to load data from FCS files into tabular format with one row per cell.

After producing the dataframe, it can be used for plotting or further analysis. We show how to produce a forward scattering vs. side scattering hexbin plot. Forward scattering vs. side scattering plots are used for gating, the first step in analyzing flow cytometry data.

Displaying an image series interactivelyDeclarative plotting