Python Flow Cytometry Calibration Library
Python Other
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FlowCal Fixed ID column name in output file with empty table. Jan 7, 2017
examples Small changes in examples' comments. Jun 23, 2016
test Merge branch 'amp_gain_FlowJo' into develop Jan 3, 2017
Install FlowCal (OSX)
Install FlowCal (Windows).bat Added MANIFEST file excluding test. Mar 17, 2016
Run FlowCal (OSX) Updated Run FlowCal files to use command line arguments. Jan 8, 2016
Run FlowCal (Windows).bat Updated Run FlowCal files to use command line arguments. Jan 8, 2016
license.txt Improved license. Jul 1, 2015
requirements.txt Changed sign in requirements.txt from == to >=. Jan 7, 2016 Increased version number to 1.0.0. Mar 23, 2016



FlowCal is a library for processing and analyzing 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.
  • Traditional transformation functions, such as exponentiation.
  • Analysis of calibration beads data, standard curve generation, and transformation to absolute units (Molecules of Equivalent Fluorophore, MEF).
  • Plotting, including generation of histograms, density plots and scatter plots.
  • A user-fiendly Excel UI to gate, transform, plot, and generate statistics from a list of flow cytometry samples in a simple fashion.


The official documentation can be found in Here you will find installation instructions, tutorials, and more.

Report Bugs

The official way to report a bug is through the issue tracker on github ( Try to be as explicit as possible when describing your issue. Ideally, a set of instructions to reproduce the error should be provided, together with the version of all the relevant packages you are using.

Request Features

Features can also be requested through the issue tracker on github. Try to be as descriptive as possible about the desired feature.