• The tSNE derived parameters now remain connected to workspace files after saving. Note: In case derivative files are ever dissociated from a workspace, drag and drop the CSV back onto the data file or right click and choose “Import Parameters from CSV/CLR”.
  • Erroneous “Unsupported Country” error message is no longer displayed when switching Locale preferences.
  • Proliferation modeling platform improvements. Making the fixed peak zero feature even more robust.
  • Figures added to the Layout Editor should no longer lose parameter annotations without user deselecting those features manually or setting them hidden in the preferences.
  • Column headers from tables in the Layout editor now render correctly when batched.
  • Figure presets fixed to apply without error messaging.
  • Reading gates from sample nodes out of .jo workspaces in FlowJo v10 is improved. Note: Tables and Layouts are not expected to convert out of .jo workspaces correctly.
  • Creating a keyword value series can now include more than 99 entries.

Known Issues

  • Export functionality including concatenations are not available for Windows users. Workaround: Revert to FlowJo v10.6.2 or update to FlowJo v10.7.1.
  • Files concatenated within FlowJo 10.7.0 may be corrupt. All FlowJo 10.7.0 concatenated files that include a time parameter are potentially incorrect and should be re-concatenated. Workaround: Re-concatenate data files using FlowJo v10.7.1.
  • Serial number authorization may take much longer to complete. Workaround: Make sure the option to use HTTPS is checked in the License section of FlowJo’s preferences.
  • 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, particularly if internet is available via proxy.
  • 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.
  • ScriptEditor is not stable, and will throw a bug reporting window if new scripts are added then old script is selected. Workaround: Don’t select previous script after creating a new script.
  • Double-clicking on a WSP file or other FlowJo workspace file will not open that workspace in FlowJo, but will instead re-launch the software. Workaround: Drag and drop the workspace of interest into an already open FlowJo workspace.
  • Changing Cell Cycle modeling constraints will not always adjust the underlying model.
  • Icons for executable shortcuts will not illustrate the FlowJo logo on Windows. Workaround: Do not be alarmed, the “Launch Anywhere” icon will still run FlowJo correctly.
  • Locale settings in FlowJo preference which indicate decimal delimiters with columns will cause a range of errors. Workaround: Use US locale settings, even in other regions to keep everything working smoothly.
  • Manual Gates set from the “Graph” tab of the Graph Window cannot be set in Windows 7.
  • The “OK” option under Manual Gating may be hidden off-screen in some cases. Workaround: Use “Tab” key functionality to move the selection onto that button.
  • Windows Only – Microsoft Visual C++ Redistributable packages may not be auto-installed on all machines by the FlowJo installer. Workaround: run the “vcredist.exe” within FlowJo’s Program Files folder manually.


  • 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.

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.


  • No plugins will be included in FlowJo’s installer by default, as of FlowJo v10.6.1. Workaround: Plugins can be downloaded and installed from FlowJo Exchange.
  • R based plugins may not 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.