FlowJo v10 provides the option to open and save your files into an ACS (Archival Cytometry Standard) container, which combines your FCS files, and the workspace, into a single file – similar to a compressed .zip file.

Why you care

As the user, the benefits of an ACS file is that your data is stored with the analysis as a unit. Hence, these 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.

The only drawback is that these ACS files do contain all your data information, so if your data files (FCS files) are large to begin with, the ACS file may take a lot of hard drive space.

More on 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.

In fact, much of the data processing presented in this journal article was done in FlowJo!


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 resaved

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

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

*Cytometry Standard (ACS) files are zip-compliant and can be opened with any tool that can process zip files. However, the data information can only be read by a program capable of processing the fcs file information, gating-ML and gating hierarchy, such as FlowJo.  For a complete list of files that FlowJo can open please see our File Types page.