You’ll notice some major improvements in this 10.0.8 release, from the very start of the application through the interface to new platforms.  In terms of user feedback, features, quality, and performance, this represents a major release and we are grateful for the many conversations with loyal users and work with beginning users whose feedback help us guide this redesign.  You will notice a significantly streamlined user experience to ease the ‘flow’ through FlowJo, improved performance on workspace opening, and a brand new signed installer package for Mac.

New Features & Major Revisions:

  • User Interface: Major overhaul and modernization of the user interface in every part of the application, prioritizing frequently used functions and improving analysis workflow.
  • Cell Cycle: Watson Pragmatic and Dean-Jett-Fox univariate cell cycle models are back, with full featured constraints and display options.
  • Export/Concatenate: Export/Concatenate has all the features you loved in v9, as well as advanced keyword-based naming and batch concatenate features.
  • Kinetics: The Kinetics Platform is back, with better time parameter handling for data from any cytometer.
  • Workspace:
    • Apply Template to Workspace. You may now apply a template and see its templated analysis and reports ‘live’ in the active workspace.
    • Cmd/Ctl S will now always save the active workspace, no matter what platform or window you have open.
    • We also re-organized the workspace right-click menu.
  • OS X version Our application for Mac is now digitally signed, and no longer requires changes to Security Preferences to run.  Installation is one drag-and-drop away.  (n.b. on Some older OS X machines, the alias file may not work on the installer dmg. To work around this, please drag FlowJo to your Applications folder.)
  • Opening Workspaces: The time it takes to open Workspaces that have complex layouts has been significantly optimized and layouts will only be loaded when accessed.
  • .jo file opening: Improvements to .jo file opening.
  • Transforms: We have added ArcSinh, Hyperlog, Logicle, and Miltenyi transform types which are also modifiable using the T-button (transform window) for much improved data display.  Also, we have added increased stability with handling older data types (FCS 2.0).
  • Plugin Architecture:  You may now use FlowJo as a platform on which to run any external algorithms for population discovery e.g. using clustering algorithms build for the statistical program R and other 3rd party applications.  You can also view your algorithm-defined populations right next to your gated populations, as gates and derived parameters.  Two examples are:
    • FlowMeans node: FlowMeans is a modified K-means clustering algorithm which can identify concave cell populations by modeling a single population with multiple clusters (Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR. Rapid cell population identification in flow cytometry data. Cytometry A. 2011).
    • SPADE Node: Spanning tree Progression of Density normalized Events is an analysis and visualization tool which organizes cells in a hierarchy of related phenotypes.  Please note that we do not provide the source for this, please see the cytospade repository and our how-to page for more details. (Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs Jr., Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, “Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE”, Nature Biotechnology, 2011.)

Reliability & Performance  Improvements:


We have made over 665 improvements and fixes to the following areas:

  • 3D Viewer
  • Boolean Gates
  • Compensation Matrix Editor
  • Compensation
  • Derived Parameters
  • Misc. Dialogs
  • FCS Scan
  • Graph Window
  • Graphs in the Layout Editor
  • Layout Editor
    • Graphs
    • Iteration
    • Output Files
    • Overlays
    • Platforms (Cell Cycle, Kinetics, etc.)
  • Plate Editor
  • population Comparison
  • Preferences
  • Printing
  • Reconnecting Samples
  • Ribbons.
  • Shortcut Keys
  • Statistics
  • Table Editor
  • Templates
  • Time Parameter
  • Transforms
  • Undo/Redo
  • Workspace


  • To save your proxy settings you will need to open the Preferences to the License Tab and enter your proxy information. Press OK to the Proxy dialog, and OK to save your prefs.

For the exhaustive list of fixes and known issues please see this page.