• Spectral Compensation option available for compensating appropriately collected data within the Compensation Wizard.
  • Platform overlays for: Kinetics, Cell-Cycle, and Proliferation now available within the Layout Editor.
  • Auto-Save workspace feature – new preference setting allows researchers to automatically save their analysis at a customizable time interval. This popular feature has been requested by many researchers, and we heard you.
  • Installing the latest version of FlowJo no longer automatically overwrites the previous install on Windows machines, and installs are now versioned.
  • Switching overlays from univariate to bivariate no longer removes previously set coloring of populations.
  • Fixed keyboard shortcuts that previously stopped working in certain workflows.
  • Color-mapping plots now do not normalize on a per population basis, and strictly utilize the scaling set by researchers for parameters within the Customize Axis dialog associated with Graph Windows.
  • Color-mapped plots now properly illustrate Large Dots and Show Grid when toggled.
  • Quad Gates now shown in Ancestry plots properly.
  • Multigraph color mapping now available for FlowJo – Allows researchers to quickly color map parameters of interest onto a bivariate plot. Particularly useful for illustrating trends across embedded spaces like tSNE.
  • CytoFlex datafiles now concatenate correctly; previously keywords were being malformed.
  • Export dialog, “Include No More Than” Downsampling option is now functional again.
  • The Logarithmic and Biex transforms now include positive decade sliders to adjust the size of an asymptotic decade in conjunction with the width basis and negative decades.
  • SampleID spreading now limited to maintain white space b/w categorical values there.
  • FACSDiva™ gating can now be exported and imported.
  • Auto-Naming column header feature now available through a special dialog.
  • Save as ACS dialog now illustrates other files in the browser.

Known Issues

  • FlowJo Portal authentication dialog cannot be closed by clicking the ‘x’ icon in the top right / left hand corner there. Workaround: Click the “Cancel” icon in order to terminate the dialog.
  • Authentication – 24-hour offline grace period (for FlowJo Site License serial number users) will not become active correctly for certain use cases.
  • Saving a workspace from a template, in the same location as the workspace from which the template was created, without name modification will overwrite the original workspace. Workaround: Make sure to name workspaces uniquely.
  • Double clicking on an ACS file will open FlowJo but not the workspace itself. Workaround: Load the ACS file by dragging and dropping it into an open FlowJo workspace, or by going through the File tab / Open dialog.
  • FlowJo does not allow users to replace numbers from a keyword value series with text. Workaround: Use the Tab key on your keyboard to traverse to the correct field for keyword entry.
  • Scrolling continuously to the end of a population name within the naming dialog can throw an error.
  • 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.


  • Changes to the scale of parameters during use of the Compensation Wizard will reset changes made in that dialog. Workaround: Set scaling of parameters prior to compensation.

FlowJo Envoy Browser

  • Clicking “No” to replace a file in FlowJo Envoy workflow will close the browser.
  • Error when opening workspaces associated with a different FlowJo Envoy region, than the one currently being used. Workaround: Only access workspaces associated with your current FlowJo Envoy environment.
  • Non-standard characters can bet entered as file or workspace names (including spaces and plus signs), which can cause problems downstream. Workaround: Make sure to use only standard alpha-numeric characters for data and analyses file naming.

Layout & Table Editors

  • Header icons will not transfer from machine to machine when sharing workspaces.
  • Batching layouts with NxN plots can cause corruption in workspaces. Workaround: Create NxN plots after batching.
  • Batched text boxes cannot be edited.
  • Control populations may lose their control status when adjusting the settings of an overlay graph.


  • R based plugins won’t function when files or file paths include spaces or special characters. Workaround: Remove spaces and special characters from data files and file paths.