Welcome to the FlowJo Utilities section of the documentation.

  • CommanJo – commanjo is a “control panel” for composing and executing FlowJo command line
  • FJDiagnostic – this utility ships with FlowJo for Windows and helps diagnose and benchmark FlowJo.
  • Txt2FCS – written originally to support “non-flow” sources of data, now integrated into the program to natively support CSV and basic image file types. Simply drag CSV or image files into FlowJo.
  • The Data De-Identification Utility, for scrubbing those sensitive bits from prying eyes.


These are a series of tools developed in parallel with FlowJo in order to help our developers study certain aspects of the software in QA testing. Since the scope of the utilities is not restricted to QA but rather the greater realm of “data handling”, we’re posting them free of charge with source code available upon request. Java.