Below are the exhaustive release notes and known issues.  For a digest of these release notes, please see this page.

Bugs Fixed

  • Improved the file saving behavior with ACS files
  • Fixed an issue where very large and complex workspaces could take a very long time to close. (A side effect of this is that you will see a dialog asking if you want to save a workspace even though it hasn’t changed)
  • Better handling of fcs files with null entries in matrix file. (rare case)
  • Fixed an issue where Layout overlays reverted to default properties when changes to legend were applied
  • Fixed a rare issue with Mo-Flo Astrios Files regarding the parameter filter string
  • Fixed an issue saving the Miltenyi Transform in Customize Axis Dialog
  • Fixed a rare issue where some data files would shows No $PnS Keywords/Labels
  • Found and fixed an error in combination gates applied (dragged) to sibling populations.
  • Fixed an issue where we were erroneously filtering out height parameters in some cases.
  • Improved the default scaling of Yeti data
  • Fixed an issue where XML Excel table export did not contain a header row
  • Fixed an issue in Population Comparison where the bin setting would be lost when the platform was closed.
  • Fixed a problem where keyboard shortcuts would not work in numeric text fields.
  • Fixed an issue where the selected parameter in the Layout Editor  graph plot where the Y axis was not displaying the full name of the parameter.


Known Issues


  • Adding fcs files to template workspace does not show Calculating on initial calculations
  • “Copy value to group” Is sometimes disabled after editing keyword.
    • Workaround: Select a different sample’s keyword field, then reselect the keyword to copy.


    • On occasion, changing Transform to Log after Compensating the Compenation group locks up the X-Axis and T button.
      • Workaround: Set your transforms before you compensate.
    • Ellipse gates do not scale with Transformation.
      • Workaround: Transform your data before adding ellipse gates.


  • Template drops panel iterated samples if a second layout is clicked, no recovery.


  • Ribbon configuration changes not saved until config window is closed.
    • Workaround: Close the ribbon window before opening a new workspace.


  • Miltenyi transform not always associated (by default) with Macsquant files


  • Plugin-managed derivative files not handled when ACS file reopened


  • Navios Data File shows no $PnS Keyword Values

Layout Outputs:

  • Layout Editor batch band – Destination button should update to reflect new path
  • layer draw problem with overlays. Using Send to Back or Bring to Front on overlapping graph windows may not bring all of the elements to the same layer.
    • Workaround: Press the Send to Back or Bring to Front multiple times until all of the elements are at the desired layer.

Layout Iteration:

  • Control Statistic isn’t Functioning in Table Editor Formulae if the columns are not named uniquely.
    • Workaround: Name your columns in the Table Editor when bringing in statistics.

Layout Editor (LE):

  • Layout Editor does not support importing images in .tiff format
  • LE graph annotation box is misaligned/not moved upon scaling plot to a larger size.
    • Workaround: Manually resize/align the annotation box when resizing graphs.
  • Odd toggle behavior with Strikethrough AND underline text properties in LE. You can choose Underline OR Strikethrough. Not both.
  • LE version of comparison node does not update when modifying the comparison node.
    • Workaround: Replace the comparison node in the LE if changes are made.
  • Mode Normalized Histograms do not Have Identical Max Peak Heights when smoothing on.
    • Workaround: Turn smoothing off when using Mode Normalized Histograms.=

Layout Charts:

  • Object Selection breaks if selected object is behind current object but the selection is within the currency selected object.
  • If the annotation font size is made larger than default,  X-Axis Numbers are Cut-Off in PowerPoint LE Plots without axes labels and annotation.
    • Workaround: Reduce the font size.


  • Kinetics time slices don’t work with synchronized groups

Graph Window GW):

  • Cannot delete quad gates in GW if another gate is present,
    • Workaround: Delete the populations in the workspace instead of the graph window.
  • PDF export of GW contains an extra blank page.
  • On OSX, Renamed file from GW export saves as non-pdf despite prefs if not extension in the saved filename.
    • Workaround: Add the .pdf file extension (as is defaulted) to the exported filename.
  • Cytoflex data defaults to -H parameters when they have been filtered out of the param list
  • Create Gates on Peaks function not working for some data files. (But works great for others.)
  • Resizing an ellipse gate with the – button in the graph window to it’s smallest size will not maintain it’s shape when using the + button to make it larger.
    • Workaround: Don’t do this.
  • Workspace navigation badges don’t update when population changed in graph window using the breadcrumb bar.
  • Using breadcrumb bar to reference an ungated pop removes “up” arrow from GW on child populations viewed in the same GW.
  • Magnetic gates arrow points away from centroid if gate bounds exceed GW.


  • Influx files exported to a new fcs file using custom parameter set has no scale for the Time parameter.
  • SVG Incompatibility with Corel Draw when exported from the  LE.
    • Workaround: Use a different file format.
  • Browse Destination does not work on macOS
  • If a concatenated file is overwritten and reloaded into workspace during open FJ session, the original file is loaded into workspace from cache instead of loading the newly concatenated output file.
    • Workaround. Remove the sample from the workspace, and then re-add it. This will clear the cache for that sample file.

Derived Parameters:

  • When opening the Create Derived Parameter dialog, a derived parameter gets created regardless of canceling by window closure.
    • Workaround: Delete the unneeded derived parameter in the workspace.
  • When nesting functions in derived parameters, you may see a syntax error even though it is correctly calculating the formula.


  • Miltenyi Compensation Matrix has Inverted values.
  • With some data files, Compensation auto-gating fails to find positive peak in bimodal distribution.
    • Workaround: Manually edit the compensation gates.
  • Mode Normalized Histograms do not Have Identical Max Peak Heights when smoothing on
  • If you are filtering out -H parameters in the cytometer prefs, FlowJo may filter out some parameters that contain the “-h” in their name. For example, a parameter named HLADR-H7 would also get filtered out.
    • Workaround: Turn off the -h filter and the parameter will be visible again

Comp Matrix Editor:

  • User defined selections in comp matrix editor reset when parameter transformation is applied.
    • Workaround: Transform first, then compensate.


  • Dongle authentication on internal network without internet in the presence of existing proxy preferences.
    • Workaround: Remove the proxy settings in the preferences, or have an alternate preference file that you use when offline by renaming a copy of the file with the proxy preferences removed.


3D Viewer:

  • 3D viewer fluorescent parameter axis values can overlap and obscure each other.
  • Z-axis label not displayed when 3D Plot is exported as a .png image
  • Z-axis of 3D viewer is displayed in wrong orientation.

Files &  Formats:

  • Saving a template with the same name as the workspace it was created from could cause the original workspace to be overwritten after opening the template into a new workspace and saving it. (The workspace created by the template is the same name as the template. If that name is the same as the name of the workspace file, then the workspace file will be overwritten when the template is opened.)
    • Workaround: Never name your template the same name as the workspace that created it.
  • Quitting FlowJo before an ACS finishes saving could cause acs file corruption.
    • Workaround: Wait until the ACS file is saved before closing FlowJo



  • Adjusting the resolution of your monitors when using more than one monitor could cause flowjo to crash.
    • Workaround: Close FlowJo before adjusting your monitor resolution.


Windows 10:

NOTE: FlowJo has not been certified on Windows 10. You may experience problems with the interface. For example:

  • Workspace icons are tiny when working with high resolution displays on windows 10
  • FlowJo Preferences windows are cut off with high resolution displays on Windows 10