10.1 has many improvements to performance, platforms, and user experience.  You should notice a major improvement in interactivity and performance with deep gating trees and Boolean gates, and we are indebted to our loyal users whose feedback was critical in delivering this release.

New Features & Major Revisions:

  • Jo file reading: Multiple improvements to .jo file reading including a fix when opening a workspace with Clone gates.
  • Export/Concatenate: fully-featured and improved keyword-based naming and batch concatenate features.
  • Cell Cycle & Kinetics: Along with other platforms, moved front and center, with multiple improvements to each platform.
  • Compensation: Parameter selector added when compensating 15 or more fluorescent parameters.
  • User Interface: Continued modernization of the user experience with fast access to Platforms; more updated icons; and re-organization of the Populations, File, and Power bands to allow easy access to Apply Template to Workspace.
  • Plugins: Multiple improvements which allow any algorithm to be plugged into FlowJo.  (Plugins will be released here and on the FlowJo Exchange in October 2015)
  • Graph Window: User can now enter float numbers in the manual gate dialog.

Reliability & Performance  Improvements:

  • Performance improvements to calculations within the workspace, opening workspaces, and significant optimization of Boolean gate calculation.  Many improvements to user interactivity while calculations are occurring.
  • Internationalization removed.
  • More than 145 issues resolved, please see the exhaustive release notes for details.


  • Enterprise Users: This version of FlowJo is not backward compatible with FlowJo Enterprise 1.4. It will work with the soon-to-be released FlowJo Enterprise 2.0.

For the exhaustive list of fixes and known issues please see this page.