FlowJo can save your analysis in 4 different ways, which are detailed below:

  1. Workspace (WSP)
  2. Template (WSPT)
  3. Archive (ACS)
  4. Excel (XLS)

1. Workspace (WSP)

The workspace is the central hub for all activity in FlowJo, and saving as a workspace will save:

  1. A list of all the samples added to the Workspace
  2. A list of all the groups that have been created
  3. All of the analyses, i.e. all gates and statistic nodes that have been added to samples or groups
  4. All compensation matrices, either acquisition defined or FlowJo defined.
  5. Keywords associated with your data files.
  6. All table definitions that you create
  7. All layout definitions that you create

For more on workspaces, please see our description of the FlowJo Workspace and reconnecting samples to a .wsp file.  Note that FlowJo DOES NOT save your FCS files as part of the Workspace.  Rather, FlowJo saves the relative path to a set of FCS files and accesses the files, as needed, each time a Workspace is opened.

2. Template (WSPT)

A template is a snapshot of your analysis without the corresponding FCS files.  Templates are very useful for repeated analysis, as the .wspt file saves your group organization (including compensation group), gating tree, and batched analysis and exports from the Table Editor and Layout Editor.

For more information, please see making and saving a template (WSPT)

3. Archive (ACS)

FlowJo provides the option to save your files into an ACS (Archival Cytometry Standard) container, which contains your FCS files and the workspace into a single file similar to a compressed .zip file.

Specifically, ACS files contain:

-One or more table of contents

-Cytometry data (FCS files) and any additional metadata files

-Version numbering of any wsp that has been changed and resaved

-Any CLR (CLassification Results) file that was created or other outputs

For more information, please see our site discussing ACS files and the International Society for Advancement of Cytometry’s document on ACS files.

4. Excel (XLS)

This will allow you to recreate your Workspace structure for use in a spreadsheet program, by saving a spreadsheet file with all columns and rows of your current workspace including all gating and statistics.