Below are the exhaustive release notes and known issues.  For a digest of these release notes, please see this page.


New Features:


  • Background calculations are much less interruptive of user interaction.
  • Boolean calculations and gate caching preference improves performance of of boolean gate calculations


UI Improvements: Updated icons across the application, optimization of bands and ribbons:

  • Populations Band: ‘mainstreamed’ the Plugins and Nodes menus out of the power Band and into the Populations Band; added a link to the FlowJo Exchange and an option to add an Open/Save Plugin to the Workspace.  Also added functions: FlowMeans, SPADE, Create Binding Node, and Apply Binding Node.
  • File Band: ‘mainstreamed’ the Apply Template to Workspace button out of the Power Band and into the File Band.
  • Reorganized the Power Band.
  • Brand New Enterprise band which includes:
    • Connect button
    • Upload Protocol button
    • Upload Comp Matrix button
    • Download Plugins button

Improved Jo file reading:

  • Workspace with clone gates may now be opened and converted
  • Other miscellaneous improvements in Jo file reading



  • If there are 15 or more fluorescent parameters, the choose parameter dialog will appear when opening the Compensation wizard to select which parameters to compensate with.


  • Significant Background Calculation Improvement

Graph Window:

  • Can now enter float numbers in manual gate dialog


  • Internationalization (multiple language translation) removed


Fixes & Improvements:


  • Fix when deleting samples while initial calculation still processing.
  • Correlation stat removed from the workspace. (n.b. Correlation plots are still available in the Table Editor)
  • Deleting a sample from a workspace with a field in edit mode fixed
  • Non-group-owned populations in WSP no longer delete one at a time with multiple pops selected
  • Multiple plugin improvements to support metadata importing 
  • Identical nodes have not been functional in previous releases and have been removed.



  • Fixed undo delete group-owned gate



  • Resetting Event# parameter scale fixed
  • Cytometer specific preferences for linear parameters fixed
  • Logicle transform render issues in the transform window fixed.



  • Time parameter Bio-Rad S3 Data fixed


Table Editor:

  • Presence of one non-time slice containing, non-copied-to-group, kinetics node may now be added to a Kinetics statistics table in the Table Editor



  • Font menu fixed (OSX)



  • Export options in Preferences fixed
  • Kinetics platform Preferences enabled


Population Comparison:

  • Help button link from Compare Populations window fixed



  • On OS X, Rich tooltip now dismisses when application loses focus.
  • Choose Parameters Dialog Lists for FlowMeans and SPADE shows stain reagent [$PnS]


Layout Editor:

  • LE Difference Table now displays differences 
  • Y-Axis Auto Scaling for Histogram Overlays is improved
  • Merged controls in population comparison now properly show up in LE
  • SVG output from LE no longer layering Gates above graph axes & Gates now appear within graph boundaries.
  • Fixes to HTML exported images of Ancestry graphs 
  • Batch to PowerPoint files fixed on OSX 
  • Panel-iterated batch output now depends on choice in the Iteration band of the layout editor.
  • Restored the ability to set a population as a Control in Overlay graphs



  • Fixed workspace closing with Kinetics
  • Y-axis scaling of Kinetics graphs when clicking “Apply” in Graph Definition window fixed
  • Kinetics windows no longer grows after each reopen
  • Batching kinetics nodes to ppt fixed


Graph Window:

  • Quadrant gates’ median markers now update with gate movement
  • TIFF export option from Graph Window fixed
  • Toggling magnetic gate fixed


File Formats:

  • Better handling of Sony FCS3.0 files
  • PNG files referenced in layouts are now included with ACS packages.


Derived Parameters:

  • Adding Derived Parameters to a Group now works in Templates
  • Some functions removed from the derived parameter dialog – n.b. all functions remaining in the menu function correctly.



  • Histogram/CDF overlays y-axis are no longer cut off
  • Y axis in Matrix Editor NxN plots now shows the correct label


Compare Populations:

  • Changed label on Compare Population Platform from Controls: to Comparators:


Command Line:

  • many Command Line batching reliability improvements
  • Command line SPADE layout histograms fixed


Boolean Gates:

  • Not gate of an And gate fixed
  • If a Boolean gate depends on a population that was removed, it no longer shows any value
  • Combo gates now displaying statistics upon initial creation


Note for 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.