FlowJo has several different output capabilities, encompassing graphics, statistics, and raw data. FlowJo supports printing from all the different views of data, as well as copying data through the clipboard or file system. FlowJo contains a special editor for the creation of Tables (statistical outputs) and Layouts (graphical outputs). The following is information regarding different aspects of… Read more »

Templates contain your entire analysis, minus the FCS files. They are the most efficient tool for repeated analyses.  A template is a replica of your workspace file without data.  It preserves groups, gates, table definitions, and layouts and allows all of that to be applied to the next data set.  A template can be created… Read more »

FlowJo  gives you the most flexibility possible with exported graphics. You can easily ungroup any graphic, and change the font attributes, line styles, etc., to make any graph look exactly the way you want in the Layout Editor. Hints on exporting graphs In the layout editor, you can copy/paste graphs to clipboard (copy/paste) to file (save… Read more »

The FlowJo workspace can be customized for frequently used operations using ribbons. The basic anatomy of ribbons are the tabs, and within each tab are multiple bands.  Figure 1 shows the FlowJo Workspace with its ribbon that organizes the features into a series of tabs, which facilitate easy navigation. Figure 1. The FlowJo Workspace Ribbon… Read more »

The contents of any window in FlowJo can be printed. To print the FlowJo Workspace window, select the Print command from the Document band. The Document band, shown in Figure 1, is by default located in the File ribbon. Alternatively, the print command can also be located in the FlowJo Home menu, shown in Figure 2. The FlowJo Home menu can be… Read more »

FlowJo’s interface is based on a Ribbon, similar to that found in Microsoft Office products. This page explains the nomenclature and properties of FlowJo’s implementation of Ribbons. A window’s ribbon is made of thematic tabs, which break into bands, which contain tasks. Ribbons become useful when organizing features in the Workspace, Table, and Layout Editors, which have previously… Read more »

Getting the good stuff inside FlowJo out for other uses! FlowJo makes exporting your analyses quick and easy. From almost every interface of the program there is a way to get your sample data, plots, or statistics out of FlowJo for use in spreadsheets, graphics programs, or almost any secondary software package. The interface areas… Read more »

Command line FlowJo is the way to use FlowJo without a user interface (“headless”) or human intervention. Using command line FlowJo, the user has various options to load data, perform auto-compensation, calculate gates and statistics, generate reports, import CLR files, export populations, and save results. Importantly, users can use command line to execute FlowJo templates… Read more »

The real power of FlowJo is its ability to batch analyses and outputs over many files. Batching, in most simple terms, is creating a list of tasks, putting them in a queue, and sending them to the computer’s CPU to be processed in order. In FlowJo that translates into something as simple as a user… Read more »

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… Read more »