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

New Features:

Cell Cycle:

  • New 1d Cell Cycle Platform with both Watson Pragmatic and Dean Jett Fox modeling.


  • Completely revised, Export/Concatenate now has all the features you loved in v9


  • New implementation of Kinetics Platform


Launcher Window:

  • New Implementation of Launcher Window


  • Digital Signature for OSX App Bundle
  • Windows Installer installs shortcut for FlowJo

Plug-In Nodes

  • R Scripts in FlowJo as ‘nodes’
  • R-nodes update when parent moved
  • R-nodes create derived parameters


  • Annotate Ribbon for TE
  • Annotate Ribbon for LE
  • Keywords icon in the TE is missing the text.
  • Layout Batch Ribbon Destination Dropdown does not resize properly for selection
  • Dropdown button widths in TE & LE should be reevaluated when values change
  • Tool Tips for Power Menu
  • Make All tabs available by default upon new install and opening. Remove Simple and Intermediate Ribbon Configuration Options
  • Button highlighting for large icons in ribbons is broken
  • Make the TE output ribbon look more like the LE output ribbon
  • Shuffle Icons in the TE Edit band
  • Document Band Re-design


Fixes & Improvements:


3D Viewer

  • Cmd S should always map to  Save workspace
  • 3d viewer, remove the save button, keep the cmd/ctl-s functionality.
  • Opening 3D Viewer from a saved WSP and ACS
  • 3D viewer Exporting confirmation
  • group applied 3D Node fixed



  • Dispatched engines
  • Offline startup improvements
  • handling any USB device as not an “”invalid dongle””
  • warning about last 4 days of SN expiry


Boolean Gates:

  • Creating Combination Gates on 5 or more gates on one sample.
  • Performance with combination gating
  • Creating NOT gate of AND population
  • Boolean gates calculation time


Compensation Matrix Editor:

  • NxN Overlay of Compensated and Uncompensated by default
  • Matrix Editor NxN plots axes
  • CSV importing to Matrix editor
  • save compensation matrix remembers last used directory



  • Navigating from Comp group to Comp sub group
  • Compensation wizard parameters handling
  • Canceling add matrix
  • Application of another matrix changes badge color
  • Compensation UI recognizes “”filter parameters” preference
  • Moving “”size”” gate during compensation


Derived Parameters:

  • Changing scale of derived parameter
  • nth Derived Parameter showing up in workspace until re-open
  • Derived parameter handling in saved/re-opened wsp
  • Derived parameter drop-down menu
  • Derived parameters and kinetics use


  • ‘Favorites’ gate name menu maintaining title
  • File Chooser now shows favorites in Mavericks (OSX 10.9)
  • Launcher window revised
  • Keyword series dialog
  • Checkbox to ‘display all keywords’ in Sample Properties dialogue
  • Preview performance in KeywordValueSeries
  • Arrow keys in fields in Transform Dialog
  • Warning Dialog for missing file.
  • Sample Inspect Dialog matrix area now visible


Graph Window:

  • Make Movie from Graph Window fixed
  • Spider Gates location/angle matches child population visualized in Graph Window
  • Miltenyi Transform now a full Transform
  • Linear axes with events for ranges that are not integers
  • Percentile gates and modification
  • Time parameter transforms, handling for Summit files
  • GW improvements in spacing, CC gate names
  • Coulter CYAN 16bit scale improved
  • Copy Histogram to excel
  • X and Y Axis Labels on graph window
  • Graph Window of Raw Samples  in Saved Workspace
  • Bisector gate optimized
  • Renamed Copy Image With Transparency to Copy Image
  • GW gate name warning
  • Statistics of derived parameter updating on modification
  • Spider Quads and transforms


Layout Editor: Graphs

  • LE and Grouped Figs
  • Multigraph Overlays
  • Show gate median appearing in LE
  • Newlines in chart annotations preserved when duplicating/batching
  • Applying Adjunct Histograms drawing
  • NxN/All Parameters by Y multigraphs maintains aspect ratio when created after histogram multigraph
  • Changing plot type for multiple LE charts
  • Graph Definition Axis Checkbox checked by default
  • LE – Send Backward and Bring Forward buttons
  • All Params by Y/NxN Mulitigraphs drawing
  • Ancestry/Backgating/NxN shows CC model & shading
  • LE Chart annotations adhere to ‘Sample Display Naming’ prefs


Layout Editor: Iteration

  • LE Batch to file with Stat Table
  • Panel iteration with kinetics


Layout Editor: Outputs

  • Replacing existing name on outputs
  • Graph labels and Numbers and handling large fonts
  • Staggered overlay output
  • Batch to Powerpoint Contour plot
  • LE Tiff output
  • Batch to Web image filenames
  • Edit text in Exported PDF Files (LE)


Layout Editor: Overlays

  • Gating issue in overlay graph
  • Remove layer command in LE legend now works to remove multiple selections simultaneously
  • Unit Area scaling in overlays
  • Overlay Legend Column Resizing saving


Movie Creation (Graph Window)

  • GW Movie Creation fixed


Plate Editor:

  • Set Plate Size dialog
  • Apply keywords to group when with multiple plates in workspace
  • Pasting Plate Name in Plate Editor menu


Population Comparison:

  • Adding control to population comparison
  • PC Layout Editor output
  • Previous / next sample arrows in platform
  • Multi-param chi square statistics
  • Add To Group function in Population Comparison.
  • Save As function in Population Comparison.
  • Progress Indicator
  • Pop Comparison Stats in LE
  • Set Control Group then Add To Group
  • Add To Group then all other selectable options from the File, Edit and View menus.
  • Comparison save as image export charts and annotation
  • Header with statistics names



  • Cell cycle prefs
  • License Prefs
  • Coulter Kaluza Gallios scale settings issue
  • Duplicate Cytometer preferences now resolved
  • Compensation Prefs
  • Plates Prefs
  • LE pref for hiding graph numbers
  • GraphsPrefs-Pane Histogram Smooth setting
  • Include Parameter Name preference effect on statistic nodes and graph windows



  • FlowJo icon is now in Header/Footer window. LE and TE
  • Reset from Print
  • Page Numbers

Reconnect Samples:

  • Reconnect workspace



Shortcut Keys:

  • shortcut key to increase/decrease gate size in GW
  • Shortcut Key for Add Staging Well
  • Shortcut Key for Save Well Selection
  • Shortcut key for Save As



  • CVs  in the TE
  • Adding a 2nd correlation stat
  • Shortcut CV statistic
  • Copy Histogram Function


Table Editor:

  • Table Keyword iteration
  • TE reports restore the Batch Type
  • Export to XML and meta data to identify samples
  • Export to HTML from the TE
  • Table Editor Expected range coloring
  • Range value display in table header cells
  • Table Editor 3D Plot window’s export
  • TE export with keyword value and handling ‘%’
  • Preference to remove summary stats in tables
  • Select all button not enabled with an empty table
  • Clear button not be enabled without a selection to clear
  • Boxplot with whiskers
  • Show header
  • Changing the Header on a sample used for a formula
  • Edited Column Headers alignment in a Batched Table.
  • TE CC column names



  • Apply Template to Workspace and transforms & matrices
  • ACS workspace name same as filename



  • Time Parameter transformation and gate scaling
  • Transform with LSRII FCS2 files
  • Legacy workspaces and time handling
  • Logicle transformation and adjustment
  • Hyperlog transformation and adjustment
  • Log on Comp Ctrl after compensating
  • Manual adjustment of arcsinh transform on CyTOF data



  • After Group Apply
  • Undo group-apply of CC node in workspace
  • Undo overlay in Grid



  • Group fields in reloaded WSP, WSPT and ACS.
  • Group deletion
  • Workspace asking to save when closing
  • Group gets locked and unable to change to another group. 60% of the time
  • Save as WSPT… now does not leave the user editing the WSPT
  • Group highlighting
  • FJ asking to save if you try to close an unsaved workspace
  • User feedback that workspace is still calculating
  • Cmd – W (Alt -W) closes the frontmost window
  • Parent sample of current graph always shows an indicator in workspace
  • Reconnecting samples to the workspace improvements
  • Opening CyTOF files
  • Edit group properties right click menu
  • Expanding Sample tree with option key
  • Remove the Group Analysis pane
  • Reorder right click menu in workspace
  • Select Equivalent Nodes now enabled when CC node selected
  • Do not open TE & LE by default when opening a workspace.
  • Re-opening a workspace that is already open
  • Keyword drop down menu in Create Series of Values
  • Workspace Editing font
  • Warning when Group is deleted
  • Cmd/Ctl S to save now works the same as pressing the Save button
  • Gate coordinates for Ellipse gates
  • Group-owned CC model constraints changed coloring
  • Numerical Keyword value series
  • Text keyword value series
  • Spacing in the rows and columns of the WS
  • dragging selection of nodes
  • Copy/Pasting a statistic from the workspace to the LE
  • Group Applied Percentile Gates deletion
  • Rename gate from right click menu in Graph window
  • OSX – Cmd W to close workspace
  • 2 monitors
  • Saved WSP appearing in recent file list
  • Group-applying ellipse gate with gate coordinates displayed
  • Gate Duplicate Feature