FlowJo Version 11.1 Release notes

Released 10.XX.2025

New Features

General

  • v10 workspaces can be opened in v11 with some limitations.
  • Keyboard accelerators have been added to allow for control of most functions via the keyboard
  • Return to launcher for workspace navigation is now an option.
  • Warning provided to Mac users who have downloaded the wrong version for their processor

Metadata Manager

  • Keyword import added to the Metadata Manager

Compensation Wizard

  • Transform properties panel is now included in the Compensation Wizard

Graph Window

  • Color axis now uses an absolute scale
  • Graphs are now high resolution
  • Downstream populations can be displayed in the graph gallery
  • Graphs can be exported as images or copy-pasted
  • Backgating is now a display option in the graph gallery

Imaging

  • CVW files can be directly read.

Reports

  • Additional plot control tools added


Bug Fixes

General

  • Workbenches with FACSDiscover data can be exported to v10.
  • FACSMelody files now load
  • Bigfoot data now displayed with correct scale
  • Engine no longer crashes if 0 event child populations are acted on
  • Engine no longer crashes if corrupt data load is attempted 

QC

  • Gates under 'Good Events' are not deleted if QC is re-run.

Compensation

  • Compensation error messages are now more descriptive
  • Size gate modifications are maintained when switching between AutoSpill and gate based compensation.
  • Graphs in the compensation Wizard no longer become empty when switching groups.
  • Program no longer crashes when new workspace is opened directly after running compensation
  • Custom transforms no longer reset  when spillover matrix is edited.

Transformation

  • Resetting the transformation no longer resets all scales to linear.

Graphs

  • Arrow tool no longer draws rectangle gate on histograms
  • Renaming quads no longer rearranges statistics

Tables

  • Multiselect populations works with stat selection

Reports

  • VCPs now display group name in legend instead of a file
  • VCPs retain group association when multiple populatios are added to Reports
  • Object snap back issue fixed
  • Floating x-axis gate label removed
  • Pasting text improved
  • Histogram range gates removed from psuedocolor plots
  • Local pref changes will update reports

Imaging

  • Image wall cell picker now scrolls to selected cell
  • Image wall performance improved
  • Large A8 files better supported

Platforms

  • tSNE performance improved

Preferences

  • Preferences apply in the correct order or Workbench > User > Computer
  • FACSDiscover default parameters correctly populate
  • Preferences are confined to specific cytometer


Limitations and high priority Issues NOT DONE YET

File operation

  • Return to launcher without saving, followed by quitting allows the user to quit without saving or a prompt
  • ID7000 data can return invalid statistics
  • Bigfoot derived FCS files are displayed incorrectly with a reduced scale
  • FACSMelody files will not load
  • Export to v10 fails for FACSDiscover data
  • Some workbenches will show the error "The file you tried to open is not supported" on attempt to open
  • On windows, files won't load from folders with accent marks in the name

Preferences

  • Preferences set on one cytometer can apply to other cytometers

Unmixing

  • In the unmixing wizard, NxN plots for BD FACSDiscover S8 data have misleading labels
  • The spillover matrix normalization approach differs from FACSDiva and FACSChorus.  Matrices will be proportionally the same, but will have different values.

Reports

  • Virtually concatenated data will display the incorrect group name in legends

Platforms

  • tSNE calculation slows down with repeated runs.
  • tSNE plots are less defined in v11 compared to v10

Image Wall

  • Large amounts of FACSDiscover data can freeze the image wall
  • Image wall filter settings reset on save/reopen a workbench