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


  • FlowJo Enterprise (deprecated) button now replaced with a FlowJo Envoy Integration Help button.
  • Updated iconography throughout.
  • Updated Java Runtime Environment – version 1.8.0_144.

Known Issues


  • This feature may fail to correctly model certain data files.
  • This tool’s outputs may not be correctly retained in saved analyses.

FlowJo Envoy Integration:

  • When saving a workspace back to FlowJo Envoy with the same name as a current file, users will be prompted, “Do you wish to replace?”. Choosing “No” will result in the FlowJo Envoy Integration browser closing.
    • Workaround: Re-open the “Save to FlowJo Envoy” option.
  • Closing FlowJo is not possible while the FlowJo Envoy Integration browser is open.
    • Workaround: Close the FlowJo Envoy Integration browser before closing FlowJo.
  • If an ACS file is saved from FlowJo Envoy the data files will at first be disconnected.
    • Workaround: Closing FlowJo and re-opening┬áthe analysis will fix this issue.
  • FlowJo Envoy workspaces opened in previous versions of FlowJo will not connect to the data.
    • Workaround: Update to FlowJo v10.4+.


  • 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.


  • Title of workspaces appended with *unsaved*, even immediately after saving.

ACS Files:

  • When saving an ACS file from an FlowJo Envoy based workspace, the default location prompt is a temporary cache folder, which will be deleted when FlowJo is closed!
    • Workaround: Save FlowJo Envoy based workspace ACS files to a known, stable local directory.
  • 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 saving an ACS file, other files in folders will not be illustrated.
    • Workaround: Search folder contents in a browser outside the ACS save dialog.
  • 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 general workaround for working with high-resolution displays on all Windows OSs. Windows users with high-resolution displays can lower the screen resolution while working with FlowJo.
    • To fix this issue in the latest release of Windows 10 – Go to your FlowJo instal folder (C:Program Files/FlowJo v10), find and right click on the FlowJo v10 application there. Select Properties from that drop-down, go to the Compatibility tab, and check the option “Override High DPI Scaling”. Lastly select System (If already selected, select Application then back to System), click Apply, and restart 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:

  • “Show Grid” and “Use Large Dots” features not currently available for color mapped plots.
  • Batched PDFs cut off the right side of plots, in certain OSX configurations.
    • Workaround: Batch into a new FlowJo workspace before saving the image as a PDF.
  • 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.



  • On a Mac, R-based plugins may fail to calculate if the file path to either the data or the workspace contains a space or other special characters.
    • Workaround: Remove spaces and special characters from file paths associated with the analysis.