FlowJo v10 provides an option to save your analysis, data, and plugin outputs as a single file.

An ACS (Archival Cytometry Standard) container file combines your FCS files, the workspace, and plugin outputs into a single file that is similar to a compressed .zip file.  ACS files can be uploaded to a server, sent to a collaborator, or generally moved around without worrying about keeping the data together since it is all contained within the ACS file.  Using .acs is a good option for any analysis that uses plugins and data stored on a remote disk, such as a server since it keeps together all of the information needed to return to the workspace. 

The only drawback is that ACS files do contain all your data so they may take a lot of hard drive space.

ACS files are zip-compliant and can be opened with any tool that can process zip files.  You can right click on an ACS file and choose ‘Open with..’ and point to any program that will open a zip file and you will be able to access the contents.  The FCS files of course, can only be read by a program capable of processing the fcs file information, such as FlowJo.  For a complete list of files that FlowJo can open please see our File Types page.

The option to save as an ACS file is available in the File band, Save As dropdown:


The ACS file format

The ACS file format was developed as a data standard by The International Society for the Advancement of Cytometry’s (ISAC) Data Standards Task Force, and details can be found in this primary research article.

Specifically, ACS files contain:

  • One or more table of contents
  • Cytometry data (FCS files) and any additional metadata files
  • The workspace which contains gating-ML, gating hierarchy, MIFlowCyt Information, and all other analyses performed as well as tables and layouts
  • Version numbering of any wsp that has been changed and re-saved
  • Any plugin output files that were created

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