Below are the exhaustive release notes and known issues. For the general release notes, please see this page.

Known Issues


  • A BD 25-color data file may not include the compensation matrix when exported from and brought back into FlowJo.
    • Workaround: Export the compensation matrix as an MTX file, and re-apply it to the exported data after bringing it back into a workspace.

ACS Files:

  • When working with ACS files, the Save As ACS command simply saves to the current ACS file instead of creating a new one.
    • Workaround: Because the ACS file contains all versions of the workspace that you saved into the ACS, you can always get back to previous versions of the workspace. If you need to create a second ACS file, duplicate it on your file system, and edit that file.
  • Double-clicking on an ACS file on Windows may not properly expand and open the ACS file.
    • Workaround: Instead of double-clicking the ACS, either drag the ACS file to any open FlowJo workspace to open it, or use the Open button in the File ribbon.
  • When saving an ACS file, it is possible to close the workspace before the file is finished saving, which produces a corrupt ACS file.
    • Workaround: Wait until the ACS file is saved before closing or quitting FlowJo.
  • When using the Cytometer Preferences to filter out -h parameters, ALL parameters that contain a -h are filtered. This may not be the desired behavior if you have a parameter with -h in the name (example: HLADR-H7).
    • Workaround: Turn off the -h filtering in the Cytometer Preferences.

Derived Parameters:

  • When creating a new derived parameter, if you choose Cancel, a derived parameter is created anyway.
    • Workaround: Delete the unnecessary derived parameter.

Display & High Resolution Display:

  • Changing screen configuration while FlowJo is running may cause FlowJo to crash.
    • Workaround: Do not change your screen configurations while FlowJo is running.
  • Workspace icons are very small when working with high-resolution displays on Windows.
    • Workaround: There is no known workaround for working with high-resolution displays on Windows. Windows users with high-resolution displays can lower the screen resolution while working with FlowJo.
  • Using certain theme configurations in Windows, the Preferences windows may have some of their content pushed off the bottom of the window.
    • Workaround: Use a smaller font setting in the Windows theme.

Graph Window:

  • Magnetic gates may have an arrow that points away from the centroid if the gate is expanded outside the Graph window.
    • Workaround: When using magnetic gates, keep all parts of the gate within the Graph window.
  • When you have a quad (or curly quad or spider quad) gate in a Graph window AND another gate, you cannot delete the quad by selecting it in the Graph window and using the Delete key.
    • Workaround: Deleting one of the quad gate populations confirms that you want to delete all four quad gate populations. Once confirmed, the quad gate is deleted.

Layout Editor:

  • For some complex layouts using NxN plots, batching may not completely render the NxN plot.
    • Workaround: There is no workaround for the batch issue, but exporting single images using Export Image in the File ribbon works as expected.
  • Some exported SVG files are not compatible with CorelDRAW.
    • Workaround: Export in other formats.
  • Copying a graph with Backgating or Ancestry turned on does not copy the entire graph.
    • Workaround: Be sure the graph is selected (not the backgating or ancestry) before copying the graph. This properly copies both the graph and the backgating/ancestry images.
  • The graph figure may be cut off when exporting to PowerPoint. For example, if you remove axis labels and hide annotation, this could occur.
    • Workaround: If anything is being cut off from the output, one way to solve this is to create an object that extends the borders of the graph. For example, putting a graph on top of a rectangle object that is larger than the graph will then extend the layout to be larger than the graph, and will capture the entire graph. (Make the rectangle white with white borders, and it will not be seen in the output.)
  • When using a Mode Normalized Histogram with smoothing turned on, the peak heights may not show as identical.
    • Workaround: Turn smoothing off.


  • When choosing a locale other than the United States in the Locale Preferences, upon saving, an “Error – Unsupported Country” warning is displayed.
    • Workaround: Dismiss and ignore the warning. The Locale change takes effect the next time FlowJo launches.