You have probably figured out that FlowJo can open FCS files from all flavors of instrument manufacturers (link). But, you may not realize that FlowJo can open a wide variety of file types for analysis, meta data, or preference related options.

Here are the file types recognized by the Workspace:

ACS files

ACS (Archival Cytometry Standard) container, which contains your FCS files and the workspace into a single file similar to a compressed .zip file.  For more information, please see our site discussing ACS files and the International Society for Advancement of Cytometry’s document on ACS files.

CLR files

CLassification Result  files are specialized spreadsheet files that define the probability a cell belongs in a certain population.  This format allows for the definition of non-geometrical populations, such as those produced by the clustering algorithms available through Bioconductor’s R libraries. Version 10 supports both the import of CLR files by drag-n-drop onto the appropriate sample, or by file-to-sample-name matching.  It is also possible to export populations to a CLR file, and to import CLR files through the command line interface.

CSV files

Comma-Separated Values files are similar to the CLR format, with the exception that the values are positive integers.  The integer value corresponds to the class of which the event is a member.

PREFS files

This file type specifies your FlowJo preferences, and can be dragged and dropped into the workspace to apply these preferences to FlowJo.

JO files

.jo files are workspaces created by the Mac only versions of FlowJo. Version 10 (cross platform functional) is not readily compatible with any .jo (workspace) files.

TXT files

.TXT files are text files, which can be dragged and dropped to the FlowJo workspace.

WEBLOC files

.WEBLOC or WEB LOCation is a Mac OS X website shortcut typically generated by the Safari Web browser which contains the URL of a Web page.  It can be used just like a URL, described below.

URL files

Uniform Resource Locator is the address of documents and other resources on the Internet.  Dragging a url (by dragging the favicon from your web browser) into a workspace will place a “SOP” (Standard Operating Procedure) link at the bottom of your workspace.

Clicking this link will take you to the website you placed in the workspace.

XML files

Extensible Markup Language has been used to structure FlowJo’s Workspace, and by going to File/Open FlowJo can open xml files.  The openness of this structured format has allowed users to easily extract data from previous FlowJo Workspaces, and we will be publishing our XML schema soon so that users can read/write workspace XML.

In FlowJo vX’s compensation editor, the compensation matrix can be saved using File/Save Matrix.  This matrix, which is an XML file, can be dragged and dropped to a sample, in another workspace for example, to apply it.

ZIP files

Zip is a file format used for data compression and archiving.  FlowJo will open all of the file types it recognizes within the compressed file.