• Dongles now authenticate FlowJo with other USB devices attached concurrently.
  • Parameter short name ($P#S) keywords now utilized in more locations, such as Multi-Graph Color Maps. This change replaces many instances of the less informative parameter name ($P#N) keywords.
  • Appropriate default scaling for BioRad ZE5 cytometers enabled.

Known Issues

  • Trouble when changes to multi-selected plots in the Layout Editor are performed.
  • Manual Gates, when set as a Control, do not contain any cells.
  • 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.
  • Kinetics time scale is not always generated correctly, particularly in overlays
  • Import/Export from Diva is unstable, and works best with BD(TM) FACSDiva version 8.5. Workaround: Use Diva version 8.5.
  • Population Comparison statistics calculated in FlowJo v10.6.1 are not correct. Workaround: Use FlowJo v10.5 for calculating Population Comparisons.


  • 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.
  • Spectral compensation involving samples with height or width parameters is prone to generate improper matrices.
  • Uncompensated parameters overlaid in Compensation Editor NxN preview are incorrectly labeled.

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.


  • No plugins will be included in FlowJo’s installer be default, as of FlowJo v10.6.1. Workaround: Plugins can be downloaded and installed from FlowJo Exchange.
  • 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.
  • 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.