This section is divided into six parts, each discussing different aspects of generating output out of FlowJo. 

A table is a text file containing one or more rows of data, that correspond to frequencies and other statistics derived from a single sample.  The table editor lets you construct the set of statistics, and then generates them for every sample in the current group.

A layout is a graphical image, composed of individual elements that represent boxes, lines, text and graphs. Elements are created by dragging populations and statistics from the workspace into the canvas of the layout editor.

Both tables and layouts can perform batch output generation using the current Group as the set of data files from which to draw information.  You should be familiar with the use of groups to use Tables and Layouts efficiently.

Printing is supported in all sections of FlowJo.  The print command has different behaviors depending on the type of window.  Specific behaviors include printing the workspace structure or single graph, as well as a set of graphs, layouts, and full report generation.

A novel feature of FlowJo is its ability to generate movies from flow data.  Any graph window can add a third dimension to the view by slicing views of the events by a third parameter.  You can also view any graph as a function of time or the event number during the sample collection.

You can also export raw data for analysis by other programs.  You can export any gated population (or the whole sample), as its own FCS file or as tab-delimited text.  You can quickly generate small subset files, optionally reducing the event count or even the parameter list.  You can use this function to reformat FCS data into spreadsheet-friendly text.

Histograms (and Cell Cycle graphs and Kinetics graphs) can be exported as well.  Here you will get two columns of "XY" data, where the first column is the channel number (or time for Kinetics), and the Y value is the event count or processed statistic.  By default, whenever you select "Copy" (or press command-C) when viewing a histogram, cell cycle, or kinetics graph, FlowJo puts two distinct items into the clipboard:  one is a graphic picture of the data (that you can paste into graphics applications); the other is a text representation of the data (that you can paste into a spreadsheet).  Sometimes graphics applications will erroneously pick the text item for pasting; if this happens to you, you can ask FlowJo not to export the text data from these graphs (via the Preferences dialog).

Finally, some notes on publication quality graphics out of FlowJo. Several nitty gritty details of data formats are explained in order to support post-processing of FlowJo's output.  Also included is the gallery of FlowJo images, as examples of what kinds of output you can create.