FlowCal is a library for reading, analyzing, and calibrating flow cytometry data in Python. It features:

  • Extraction of Flow Cytometry Standard (FCS) files into numpy array-like structures
  • Traditional and non-standard gating, including automatic density-based two-dimensional gating.
  • Transformation functions that allow conversion of data from raw FCS channel numbers to arbitrary fluorescence units (a.u.).
  • Plotting, including generation of histograms, density plots and scatter plots.

Most importantly, FlowCal automatically processes calibration beads data in order to convert fluorescence to calibrated units, Molecules of Equivalent Fluorophore (MEF). The most important advantages of using MEF are 1) fluorescence can be reported independently of acquisition settings, and 2) variation in data due to instrument shift is eliminated.

Finally, FlowCal includes a user-fiendly Excel User Interface to perform all of these operations automatically, without the need to write any code.

Cite FlowCal

If you use FlowCal in your research, we would appreciate citations to the following article: