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Full Version: Using Python to read and analyze flow cytometry data files
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Has anyone ever used Python to read and analyze flow cytometry data files? If so, would you be willing to share the program or script? If not, it might be an interesting project for a student. The file data structure is standardized, and descriptions of the data file standard are readily available. Thanks...dtm, email:
there are plenty of packages available
I maintain several Python libraries for interacting with flow cytometry data (FCS files):
  • FlowIO: For reading/writing FCS data. Meant for low-level interaction with zero dependencies on other libraries.
  • FlowUtils: For basic flow cytometry operations, including compensation and transformation (with support for the logicle transform)
  • FlowKit: A Python toolkit for flow cytometry analysis and visualization, including GatingML 2.0 support.

FlowKit is the most recent addition, and probably the most useful. All of these are based off of the original FCM library.
Honestly, I haven't even heard of it, but this is awesome!