Getting data out of FlowJo is helpful for a variety of tasks in flow analysis. You may need to create new FCS files, save workspaces or templates, recreate histograms in a spreadsheet program, or add files together (concatenate) to help in identifying rare events or add to your laboratory notes by getting file keyword values out of the workspace.

From the workspace you can export your data as a new FCS2, FCS3, CSV, CLR, or NETCDF file. You can also export your Workspace structure (gating tree and all columns) for use in a spreadsheet.

The following section describes how to export data directly from the workspace using the Save As and Export options within the Document ribbon.

To generate a template or save a workspace you may choose to save a WSP, WSPT, or ACS file. Click here for more information about saving in these file formats.

You can also export data directly from the Graph Window.

To learn about exporting data from the Table Editor click here.

To learn about exporting data from the Layout Editor click here.

Export Data as a New FCS, CSV, CLR, or NETCDF

Highlight the files in the workspace you would like to Export (e.g. the first five files in the sample below).

Select Export from the File tab in the workspace, the following dialog window will appear (one or more samples need to be selected for Export to work).


This dialog allows you to export a subset of the parameters of the file if you wish. Uncheck any parameters you do not want in the exported file.

Event Count

The number of events in the file (or files if concatenating) to be exported will be displayed here. You can chose to export a representative subset of the total by specifying a smaller number in the Event Count box. In this case, FlowJo will randomly remove events from the file until the specified event count is reached.


Select between CSV (Comma Separated Value), FCS2, FCS3, CLR, or NETCDF for the appropriate file format of the exported data.

You can export data for a selected population in three ways.

  1. In the form of a new FCS file containing only the data you want to include. (FCS 2.0 files can be generated from either FCS 2.0 or FCS 3.0 files, but FCS 3.0 files can only be generated if the original file was acquired in the FCS 3.0 format)
  2. As a file containing a list of Comma Separated Values (CSV) that can be imported into a spreadsheet program.
  3. CLR file (CLassification Results) – a CLR is a valid csv spreadsheet file, where each row corresponds to an event in the sample file. Each column corresponds to a ‘class’, where the value is the probability of the event being a member of the class, i.e. a value between 0 and 1.  The first line may optionally contain class names.  If the probability values are either 0 or 1, then the the CLR file is said to have ‘definite’ class assignments. Read more here.
  4. NetCDF file (Network Common Data Form) – a part of the ACS standard, NetCDF makes use of a widely used, free set of libraries that allow for visualization of scientific data. This format stores all event/particle information in array form.

The exported FCS files can then be read by any other application that can read FCS files including being reloaded into FlowJo. This is useful if you are working with very large data files and only need to examine a small subset of the events: exporting them to a separate file will usually make analysis faster and more efficient.


To concatenate: highlight samples in the workspace, click on the Export button in the File Tab, in the export dialog box, check the box to concatenate. Select Format and click Export. These files are now grouped into 1 file.

Exporting to Excel

If you would like to recreate your Workspace structure for use in a spreadsheet program, choose Save As… XLS Excel from the Workspace “home” button or from the File tab. Exporting to a spreadsheet file will export all columns and rows of your current workspace including all gating and statistics.