FlowJo accepts a variety of file types in addition to Flow Cytometry Standard (FCS) files.

Opening Sample and Other Data Files:

  • FCS Files: FlowJo accepts FCS files from nearly all cytometers. To load files into FlowJo, drag-and-drop a folder of files onto the Workspace window, or click the Add Sample button (below) to get a file navigation window, browse to your folder of files and click “Choose”. To learn more about FlowJo and data scaling for data from your cytometer, please visit FlowJo and Your Cytometer.
  • .WSP and .JO Files: FlowJo can open .WSP and .JO files with your previously saved analyses. If you are opening an old workspace and need to reconnect your files, please visit this page.
  • .ACS files: Analytical Cytometry Standard files can be created and opened with FlowJo.  These files compress the analysis files, the plugin outputs, and the data files into a single .ACS file.  ACS files can be unpacked simply by dragging them into a FlowJo workspace.
  • Other File Types: For a full list of supported file types including .CSV, .PREFS, and .ZIP, please see our list and descriptions of accepted file types.

Examining and Exporting Sample Data:

  • The Sample properties of each sample may be examined from the workspace by clicking on the circle badge next to sample name.
  • Sample and gated data can be exported for further analyses.