• Improved calculation speed:

The figure above shows the recalculation times for a variety of workspaces that vary in number of samples, size of samples, and complexity of analysis. We can conclude from this plot that  v10.8 will provide a nominal performance boost to most data sets, but that boost becomes increasingly significant with larger data sets, particularly those comprised of a large number of small files and many gates.

  • Spectral compensation: FlowJo to this point has normalized all compensation matrices to the ‘diagonal’, meaning the value in the primary detector. For traditional compensation approaches this will always be the largest value and the resulting diagonal will be 100% of the signal for the given fluorochrome. In spectral compensation, where there is no longer a 1:1 relationship between number of detectors and collected parameters, the largest fluorescence value may not be in the primary detector. FlowJo continued to normalize to the ‘primary’ detector and allowed for larger numbers. Spectral compensation in BD FACSDivaTM instead normalizes to the largest number. Importantly, neither of these approaches are wrong; fluorescence values are relative, and all measures would remain relatively the same, so there is no need to re-analyze spectrally compensated data. However, as we work toward better alignment between all software in our control, we have chosen to align the two compensation methods and normalize to the largest number. This will allow for better interoperability between BD FACSDivaTM and FlowJo users.
  • Jo file reading: FlowJo version 9.x produces .jo type files as the analysis output. Version 10.8 will be the best version of 10 to directly open .jo files with to convert them to .wsp files. A handful of XML reading adjustments were made to translate group membership better, align time parameter reading, and handle multiple files with the same name.
  • Improved FlowJo Portal Sign In: There is now a ‘Show Remember Me’ check box in the license preferences.  When checked this will reveal a check box that allows the user to have FlowJo remember the FlowJo Portal credentials they used to sign in for 24 hours.  Additionally, HTTPS for authentication is checked on by default.
  • Bug fixes:
    • Hiding rows in the compensation matrix no longer causes editing offset issues.
    • Boolean gates dragged within a sample no longer reference the original population.
    • Exporting offset histogram overlays to pdf no longer pushes the histogram off the graph
    • Ancestry plots are now printed to PDF
    • Copy gate to group no longer overwrites modified downstream gates.

Known Issues

  • Files saved at a remote location can cause a variety of errors when reopening the analysis after saving. Workaround: Reconnect remote files that cause problems by right-clicking on the file name in the FlowJo workspace and choose Search for FCS files…
  • FlowJo does not allow users to replace numbers in a keyword value series with text. Workaround: Use the Tab key to traverse to the correct field for keyword entry.
  • 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 FACSDivaTM version 8.5. Workaround: Use BD FACSDivaTM version 8.5.
  • ScriptEditor will throw a bug reporting window if new scripts are added after an old script has been loaded.  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.
  • 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.
  • Individual FCS files larger than 3 GB can appear to have no events when plotted.
  • FCS files with only 1 event can display the fluorescent value incorrectly.
  • Keeping an expired serial number entered in the licensing preferences will prevent a dongle from authenticating. Workaround: Delete the expired serial number from the licensing preferences.

Layout & Table Editors

  • Batching layouts with NxN plots can cause corruption in workspaces. Workaround: Create NxN plots after batching.
  • Batched text boxes cannot be edited.