FlowJo Version 10 provides a number of advanced features that can be used to integrate FlowJo with external laboratory information systems and automated scripted analysis.  These features include the following (click on any of the links to be taken to a page with a more detailed description of the feature):

Command line FlowJo

FlowJo can be executed by a command line shell script to perform a variety of functions without a user interface or human intervention.  The interface has various options to load data, perform auto-compensation, calculate gates and statistics, generate reports, import CLR files, export populations, and save results.

Support for cluster result files (CLR)

Cluster 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.

Server-based FlowJo

FlowJo can be deployed in a web server so that users can perform analysis using FlowJo’s calculation engines that reside on a remote server.  The FlowJo server loads data and performs calculations for multiple users, distributing requests across multiple engines and managing user sessions and cached data.  In addition, the server also supports higher level operations to save FlowJo templates and workspaces on the server, and to execute command line FlowJo to generate analysis and reports which are available on the network.  The enhanced FlowDx server supports the creation, distribution, and aggregation of FlowJo workspaces to make statistical comparisons of different analysis techniques.  This server utilizes an SQL database to store meta-information about assays, target populations, and cluster results.

Plug-in server integration

It is now possible to hook into FlowJo by writing your own java module that is executed when a workspace is opened or saved.  By implementing a simple interface, the custom code can access the xml attributes of a FlowJo workspace that includes gating and statistic results, and can perform additional operations such as writing these results to an external database.

Remote data file references

Data files that are located on a remote data server can be loaded into FlowJo by using an ‘http:’ URL reference.  FlowJo manages the downloading and caching of the data files to the local computer so they can be used by FlowJo.  FlowJo also supports another kind of reference to a data file, an ‘fjref:’ URL, where the data remains on the remote server and is accessed through a FlowJo server.  A file containing a list of remote data files can be loaded as a workspace, and can be used as the input data set for command line execution.

Enhanced support of Archival Cytometry Standard (ACS) files

An ACS file is a specialized zip file that contains the fcs data and analysis files.  When a FlowJo workspace is saved as an ACS file, the zip file includes all the data files, a GatingML definition file for each data file, a table of contents, and a new version of the FlowJo workspace.  When the ACS file is opened, FlowJo looks for the most recent version of a workspace to open.  If the user imports CLR files to a workspace, the CLR files are also added to the zip file and the table of contents is updated.  Each time the ACS file is saved, a new version of the FlowJo workspace is created and older versions are retained in the zip file.  ACS files can be opened and saved using command line FlowJo.