FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data.

  • Archival Cytometry Standard (ACS) are container files that compress workspaces, FCS data files, and plugin outputs into a single compressed .zip file, helpful for archiving, sharing, or working with remote data storage.
  • Templates are an excellent way to expedite data analysis by applying a previous analysis to new data.   A template contains the groups, gates, and statistics without the associated FCS files for re-use.
  • R-tools provide additional functionality for complex data analysis. 
  • Dimensionality reduction is a means of creating mathematically derived parameters that represent the collected parameters holistically, providing excellent visualization of high-dimensional data or clustering results. 
  • Command line  FlowJo is a means of running FlowJo “headlessly” without human intervention.
  • Script Editor is a tool that allow for users with JavaScript skills to interact programmatically with FlowJo to produce automation routines. 
  • De-identification utility is a stand-alone tool that allows users to strip identifying information out of FCS files to preserve privacy.