New Features

Note:  This version of FlowJo is NOT compatible with FlowJo Enterprise. Stay tuned for the upcoming FlowJo Enterprise release that will work with this version.

New FlowJo Plugin Architecture.  

FlowJo can now use plugins that can perform a variety of functions, including the creation of populations, creation of derived parameters, and actions when opening or saving a workspace.


We will soon be releasing developer documentation on the FlowJo Plugin API including sample code to help understand how to write these plugins.


The FlowJo plugins provided with this release include:

Plugin Description System Requirements Documentation
CellOntology-1.0.0.jar The CellOntology plugin allows you determine the name and etiology of a gated cell or population in question. FlowJo, R & BioConductor Tools Documentation Link
DownSample-1.0.0.jar Downsampling is the process of selecting a limited number of data points/events from a sample or gated population. A new Downsample Gate is created containing the selected subset of events, which can be used like any other gated subset or population node within FlowJo FlowJo Documentation Link
FlowMeans-1.0.0-beta.jar Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required. FlowJo, R & BioConductor Tools Documentation Link
Spade-1.0.0.jar  Spanning tree Progression of Density normalized Events (SPADE) is an algorithmic visualization tool for high-dimensional flow and mass cytometry data. SPADE takes in FCS files and settings, and outputs a network graph file (GML), PDFs of the graphs, and FCS files with the “cluster” column appended. SPADE is implemented as a program in the R statistical computing environment. Therefore, to use SPADE, you must install R and the required R packages onto your computer. Once installed, you will no longer need to open R to access SPADE in FlowJo, In FlowJo 10.1r7 SPADE is run as a Plugin, which takes a gated population from FlowJo and runs SPADE within R to generate the associated derivative files. For more information on SPADE, please see the references below, or visit the cytospade repository. FlowJo, R & BioConductor Tools Documentation Link
TSne-1.0.0.jar  T-Distributed Stochastic Neighbor Embedding (tSNE) is an algorithm for performing dimensionality reduction: the visualization of complex multi-dimensional data in fewer dimensions while still maintaining the structure of the data. FlowJo, R & BioConductor Tools Documentation Link


Additional Features & Improvements.  

  • Increased the number of parameters that FlowJo can analyze to 1000
  • Added a field to allow specification of R’s path in prefs (Diagnostic Panel)
  • Improved the interface for Licensing Preferences Panel in the case where a computer has many hardware addresses.
  • Updated EULA to raise the awareness of the fact that you may not install FlowJo on a Virtual Machine.
  • Unchecked ‘Display other X/Y parameters than in parent plot’ as default in Gates Preferences
  • Removed the option to downsample when concatenating files. (downsample before you concatenate if desired.)

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