FlowKit Documentation

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FlowKit is an intuitive Python toolkit for flow cytometry analysis and visualization, with full support for the GatingML 2.0 standard and limited support for FlowJo 10 workspace files.


  • Read FCS files, including versions 2.0, 3.0, and 3.1
  • Export FCS data as a new FCS 3.1 file, NumPy array, Pandas DataFrame, or CSV
  • Compensation of FCS events
  • Automatically create compensation matrix from compensation bead files
  • Tranform FCS events in a variety of transforms used in the flow community (including logicle)
  • Full support for the GatingML 2.0 specification
  • Limited support for importing FlowJo 10 workspace files. Workspace files are currently limited to the following features: * Linear, logarithmic, and logicle transforms * Polygon and rectangle gates
  • Programmatically create gating strategies including polygon, rectangle, range, ellipsoid, quadrant, and boolean gates
  • Easily retrieve gating results from a gating strategy as a Pandas DataFrame.
  • Optional, automatic filtering of negative scatter events and/or anomalous events
  • Visualize FCS data as histograms, contour plots, and interactive scatter plots