• New native tSNE platform. Note: This does not replace the legacy tSNE plugin (as that will be required as an object within FlowJo’s plugin folder) but is a preferable method of calculating derived parameters, due to its supremely improved performance.
  • Derived parameter fixes.
  • Memory management issues fixed.
  • Native tSNE now runs correctly on grandchild and deeper subpopulations.

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.
  • Browser for saving an analysis as an ACS file only illustrates folders, not files.
  • 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.
  • Export population dialog’s #Events to include option is grayed out. Workaround: Use the DownSample plugin to reduce the number of events utilized in a given population.
  • 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.
  • Installing FlowJo using default settings on a Windows OS after a previous version is installed will cause a corrupted installation. Workaround(s): Delete the Program Files folder for FlowJo prior to installing a new version. Alternatively, add a version number to the new install folder for FlowJo, within the install wizard.

Color Mapping

  • Options to “Show Grid” and “Use Large Dots” are not functional in color mapped plots.
  • Color mapping is always normalized to the population being viewed.


  • 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

  • Workspaces containing FlowJo Envoy data won’t open correctly in older releases. Workaround: Update FlowJo to v10.4+ if you need to access analyses associated with FlowJo Envoy data.
  • 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.
  • Saving ACS to FlowJo Envoy platform will default to a cache folder, which will be deleted when FlowJo is closed. Workaround: Save FlowJo Envoy based workspace ACS files to a known, stable, local directory.

Layout & Table Editors

  • Closing and re-opening the layouts dialog disables keyboard shortcuts.
  • 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.
  • Quad gates aren’t illustrated in ancestry plots.
  • Batched text boxes cannot be edited.
  • Control populations may lose their control status when adjusting the settings of an overlay graph.

Plate Editor

  • The plate editor will not always succeed in applying keywords from file to samples.

More Info:

Please direct any questions on FlowJo to: techsupport@flowjo.com