• Improved authentication. The HTTPS connections to FlowJo Portal for authentication/authorization purposes can be secured by either a FlowJo SSL certificates or newly by an SSL certificates installed by the end user’s corporate security or IT.
  • Total Spread Matrix (TSM) is now available for matrices created in FlowJo. TSM is the Spillover Spreading Matrix (SSM) without normalization to the florescent intensity of the probe. Panel designers consider the brightness of a dye as well as its spread as factors impacting that ability to separate populations. These factors are combined in the SSM metric, but de-coupled in TSM so that the designer may factor in the total spread introduced into a panel apart from brightness. This new measure is available in the SSM dropdown in the Compensation Editor.
  • Overlapping curly quad boundaries corrected.
  • Improved support for LMD files.
  • Improved handling of v9 files.

Known Issues

  • Authentication – 24-hour offline grace period (for FlowJo Site License serial number users) will not become active correctly for certain use cases, particularly if internet is available via proxy.
  • When creating a keyword value series, and replacing numeric entries with text, the text entry box cannot be selected via mouse click.  Workaround: Use the Tab key on the keyboard to move to the correct data entry box.
  • Proliferation nodes applied to a group will not have the same functionality compared to group owned gates, i.e. proliferation nodes applied to synchronized groups will not adjust automatically when one node is altered, and the color/font-style of proliferation nodes will not match their group.
  • Import/Export from Diva works best with BD(TM) FACSDiva version 8.5. 
  • Double-clicking on a WSP file or other FlowJo workspace file will not open that workspace in FlowJo, but will instead re-launch the software. Workaround: Drag and drop the workspace of interest into an already open FlowJo workspace.
  • Locale settings in FlowJo preference which indicate decimal delimiters with commas will cause a range of errors. Workaround: Use US locale settings, even in other regions to keep everything working smoothly.
  • Manual Gates set from the “Graph” tab of the Graph Window cannot be set in Windows 7.
  • The “OK” option under Manual Gating may be hidden off-screen in some cases. Workaround: Use “Tab” key functionality to move the selection onto that button.
  • Spectral compensation involving samples with height or width parameters is prone to generate improper matrices.


  • R based and Java plugins may not function when files or file paths include spaces or special characters. Workaround: Remove spaces and special characters from data files and file paths.
  • Derived parameters generated from plugins can be lost after a workspace is saved. Workaround: Export FCS file(s) on which plugins are run including all derived parameters there, and re-import the exported files for downstream analysis. Alternatively, the derived parameter .csv files can be found in the derived parameter folder created by the plugin and they can be drag and dropped onto the sample to reconnect the analysis.