There are several potentially interesting things you might want to do with this data:

• Print it one layout per page as a report 
• Print it at a minimum readable size for summary analysis
• View it as tiled graphs onscreen
• View it as a movie onscreen
• Save a standard Pict file for further processing / publishing
• Create a website showing all images
• Create a website including the movie

The window that supports all these functions is called the Stack Viewer.  As the layout editor iterates, it builds a series of frames.  The collection of all the frames is called a stack.  FlowJo supports two different mechanisms to visualize a stack onscreen:

Both views support outputing the graphic display to disk, clipboard, or printer.  These functions can be accessed by the menu commands (under the "File" menu), the command-key equivalents (command-S, command-C, and command-P, respectively), or by clicking on the appropriate icons near the top right of the Stack Viewer window.

The Custom Layout Options dialog handles special case scenarios where you want to determine the layout from a fixed number of rows instead of a fixed number of columns. It allows you to order the graphs from top to bottom instead of from left to right.

You can enter a value for either dimension, and the other side will be automatically recalculated to accommodate the number of frames in your stack.

"Order successive samples" is a way to determine how the frames are sequenced, as illustrated by this picture (left).

These options are found in the Page Break Popup, located at the bottom of the window.  The first options No Page Breaks, will let the printer handle everything as it normally would.  The second option, Show Breaks, draws light gray lines to show page breaks, but does not change the frame placement.  The third option, Avoid Page Breaks will spread out the tiles to minimize the number of graphs crossing a page boundary, without changing the size of the frames.  The final option, Scale To Page, will resize the graphs so that the specified number of rows or columns fits exactly into one page.  (This doesn't force the entire output to fit onto a single page, only that one full row in direction in which you are ordering successive samples will fit.)

The human eye and brain are better suited for finding patterns changing through time than they are in juxtaposing patterns in a two dimensional grid, or in constructing them in a three dimensional space.  If you are searching through a large number of samples looking for patterns, similarities or trends, this animated view may give you a new approach to try.

Since the data for the animated frames and tiled frames are based on the same graphs, you can quickly switch between the views without have to recompute extensive numbers of graphs. As you switch between the view, you'll see that many of the controls are different.

Across the bottom of this window are the standard controls used to play a quicktime movie.  The leftmost arrow is the play button.  The right side controls move to the previous or next frame in the movie.

There are also keyboard shortcuts for each of these actions:

The space bar (or double clicking the frame) will play the movie.  The left and right arrow keys move to previous and next frame.

It is possible to export movies to other Mac programs or web sites by dragging the image from the window to the Finder.  Shift click on the thumb of the scroller to select a subrange for export.