FlowJo v9 Manual


Version 9.9.6 Release Notes

  • Note: Workspace file format has changed – workspaces created in 9.9.6 cannot be opened in older versions of FlowJo.  (Save as XML to read in older versions)
  • Features:

    • Population comparison platforms allow selection of tSNE, LDA, and PCA parameters
    • New platforms:
    • Bivariate Difference Gating (BDG): 
    • Compare two parameter plots, such as tSNE maps, and gate on the differences.
    • List Value Gating: 
    • FCS files concatenated by FlowJo from multiple files can be sub-gated to select groups of files from similar samples.  For example: concatenate clinical specimens, and then gate on all data from only control subjects, or only female subjects, or any other criteria).
    • Mapped BDG:
    • A combination of List Value Gating and BDG that allows you to compare and gate on differences between groups of subjects.


    • Improved stability
    • Proliferation analysis copy to clipboard includes replication index
    • Overlay nodes are properly saved and read in XML files
    • Custom compensation matrices are properly read from XML files

    Known Issues:

    • Adobe Acrobat is unable to open PDFs created by FlowJo v9.9.6. We recommend using any other PDF viewer.

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