For more information about each type of preference, click on the topic:

• Workspace
• Graph
• Gate
• Layout
• Export

FlowJo preferences are stored in the System Preferences folder.  If the program ever has problems running, even before it tries to open a workspace or view any data, then it is useful to try removing this file from the preferences folder, restarting and letting FlowJo recreate this file from scratch.

Workspace Preferences

The first section, "Saving & Restoring", relates to preferences regarding the workspace document. By entering a non-zero value in the box, you instruct FlowJo to remind you to save the workspace every few minutes. When this amount of time has elapsed, FlowJo puts up a dialog and lets you choose to save or not to save the workspace (note that this dialog has a checkbox that lets you specify to always use the same answer:  if you check this box and click "Yes", then FlowJo will automatically save the workspace for you every time period that you select here). If the "Reopen graph windows..." option is checked, then FlowJo will automatically re-open all graph windows that were open when you last saved the workspace.  Finally, for some sites, FlowJo retrieves data over the internet; in these cases, you can select a maximum cache size that FlowJo uses to keep copies of the data on your Macintosh (and, if you desire, to have FlowJo delete the cache files when you quit).

The section, "Appearance" defines preferences about the how the workspace appears. First, you can have FlowJo show you a "thermometer" bar displaying the amount of free memory available to FlowJo (if you encounter problems with the program and this bar is consistently full, or red in color, you might consider increasing the available memory). You can also have FlowJo show you a time counter, showing the elapsed time since you saved the workspace. The memory monitor and the time counter are shown in the tool bar of the workspace. Further options let you choose to have FlowJo display a light grid over the sample and group list to aid in visualization.  You can also choose to have FlowJo the sample's file name as it is on the system disk rather than an internally-defined value (for the sample title). If you don't select this option, FlowJo examines the FCS header and selects one of the keywords related to the sample title for display.  The setting "Gate Statistic is Freq. of Parent" allows you to specify that the percentage shown in workspace refers to the portion of the immediate parent population, as opposed to the portion of all cells. "Copy $Comment to annotation" will cause the keyword of comments made during acquisition to be turned into an analysis annotation. These settings apply immediately, to all open workspaces and to workspaces you will open in the future.

If you click on "Use As Default", then FlowJo records the columns & spacing that you have set in the current workspace, and uses that for all new workspaces that you create.

The next section, "Drag & Drop", controls how FlowJo causes recalculation of gates & statistics that are copied between subsets (or samples) to occur.  The default behavior, "only if sample loaded", will cause statistics to be computed only if the sample has already been read into memory (and still resides in memory).  You can also choose to have the statistics compute immediately (which may cause FlowJo to need to load the sample data), or only when needed.  FlowJo will always compute the statistics once they are requested by the Table Editor or Layout Editor... this option is designed only to control the calculation of statistics for display in the workspace window.

The final preference in this panel governs the Task Monitor, the window that shows status of on-going calculations. You can pick which location on the screen where the task monitor will appear, or instruct it not to appear at all.

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Graph Window Preferences

These preferences define how a graph window should look when you first open it. The different window sizes present different amounts of information; you can choose between small, medium, large, and resizeable graph windows.

The font information is applied to axes numbers and labels, both in the graph window as well as any exported graphics (i.e., when you copy graphs to other programs or generate Layouts). 

The graph type and options are identical to those you can specify in the floating graph specifier window. This will be the default graph displayed whenever you open a sample for the first time.  "Forward scatter on x...", when checked, specifies that FlowJo tries to show Side scatter vs. Forward scatter the first time you open a sample's data (otherwise, it tries to show Forward vs. side scatter).

The "Miscellaneous" section groups a few other preferences together.  "Show live quadrant statistics" specifies that FlowJo should calculate quadrant statistics whenever the quadrant tool is selected. If unchecked, the statistics are not displayed in the graph window while you track a quadrant gate.  "Hide Graph Tools" specifies what to do with the Graph Specification Window whenever a graph is not the front-most window; you can either hide the floating window or simply grey it out.  "Show gate frequencies on plots" specifies that FlowJo should draw the frequency (within the parent gated population) of any gate drawn on a graph.  The frequency is drawn in percent.  The frequency is drawn on exported graphs whenever the gate is drawn, if this preference is selected.  You can choose the maximum number of dots to draw in a dot plot. If you use dot plots (and in general, you shouldn't!), and you have more than 10,000 events in a file, you may wish to limit the number of dots drawn to speed up display or to keep it from "blacking out" completely.  Finally, you can choose to draw "large dots", applying to both Dot Plots as well as Contour Plots with outliers.  These dots are twice as large in each dimension, and may be easier to see on slides or publications.

The final section relates to the Compensation Platform.  Often, software compensation causes data to be compressed onto the bottom or left axis in displays.  This can be un-aesthetic... if you desire, you can specify that FlowJo increase the dynamic range of compensated (logarithmic) parameters by added 1/2, 1, or 1 1/2 decades of dynamic range to the bottom of the parameter.  This may improve the visualization of compensated data.  When you change this value, it will apply to any compensation computed in the future.

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Gating Preferences

The third set of preferences specifies what will happen when you draw a gate and create a new population. The graph for the new population will either have the same parameters as the graph on which you drew the gate; or, if the box is checked, FlowJo tries to intelligently select a new pair of parameters to display. The graph type itself is selected by the pop-up menu. Here you can select that the new graph type is either (1) the same as the graph on which you drew the gate; (2) the same as you specified in the preferences section above; or (3) a blank graph. The latter is useful when you are working with enormous data files, where you would like to specify the graph before FlowJo takes the time to calculate it for you.

"Auto-select gating tool...": when selected, a new gate is started whenever you click in an "empty" area in a graph window (this is the way early versions of FlowJo operated). The default gate type is a polygon; if you option-click, then a rectangle will be created. If this option is unchecked, then FlowJo does not auto-select a tool when you click in a graph window; rather, you must select the tool from the floating graph specification window.  If  "Auto-set Tinted" is selected, then any new gate is tinted by default.  You can change the tinting of a gate by using the Graph Specification Window.

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Layout Preferences

The option "Export Short Statistic Names" causes an alternate set of statistic names to be used in the creation of tables.  There is a tendency for the first row of tables, which contains the column headers describing the statistics, to become long and unwieldy.  This setting will reduce that effect.

Within the layout editor, double clicking on most items, or choosing the Get Info… command from the menu will edit that items specific attributes. If multiple items are selected, then a "multiple item settings window" comes up which contains all of the settings available. Setting this check box will cause the larger dialog to be shown all the time.

The "Use Placeholders" setting will create new layouts so that they only show the box enclosing a graph (and its legend and annotations) instead of actually plotting the data.  If the layout is complex or references large data sets, the recalculations in the layout can be quite slow.  Using placeholders will speed up of the response time.  This option is also available within the layout window itself.  This preference will determine its default state.

"Prefer Tiled Frames" determines which view comes up first when looking at a stack of generated layouts.  If this box is checked, the Tiled Frames view will come up first.  Otherwise, the Animated Frames view will default to be the first visible.

"Allow Stain Name Mismatch" loosens the strictness on matching gates across samples.  Normally a sample must match both the parameter and the stain name in order for its graph to be included in a layout.  If this setting is on, then only the parameter name is required to match.

"Back & Forth Looping" directs the movie viewer in the layout editor to loop such that they play a movie from beginning to end, and then play it backwards from end to beginning.  If this is not set, the movie will play from beginning to end and then jump back to the beginning and play it again.

There are a series of preferences dealing with the information that accompanies a graph in a layout.  These determine whether the information (the Annotation) is shown at all, and if it is, which information and statistics are included.  The graph's title, the name of the sample, and the list of parent gates (ie, the path name), as well as the population's frequency and event count can all be included or excluded independently.  In addition, you can determine the default font, size, justification and color of the text in this box.

Finally you can set preferences for text boxes that you create directly in the layout, or that are created when you drag statistics from the workspace window into the layout.  These settings include the font, size, style, justification and color of the text.  The checkbox "Draw Border Around Text Boxes" determines whether a line is drawn around the text boxes by default.  All of these settings can be overridden within the layout, by selecting the text box and choosing Get Info… from the Layout menu.

Each of the Layout Editor and Table Editor have buttons that will cause the current output to be written to a file and launched by a different program. For the table editor, you can pick a spreadsheet or statistics package. For the layout editor, you can pick a graphics or publication program. Use the Choose... buttons here to pick the applications you wish these buttons to launch.

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Export Preferences

The first section of this pane specifies what to do when you copy graphics into the Layout Editor or into other programs for presentation purposes.

The "Include gates..." option specifies whether gates on a graph are copied into exported graphs by default. When you press the option key while selecting "Copy", this attribute is toggled. "Include text data…", if checked, causes FlowJo to put two distinct items on the Clipboard whenever you select "Copy" from a Histogram window (or a Kinetics window): one is the graphic, the other is a text representation of the processed data. Depending on whether you copy into a graphics program or a spreadsheet, you will get the appropriate item. (Some graphics programs incorrectly prefer text when pasting; if this is the case, select this checkbox to have FlowJo only copy the graphic).

You can choose between four common file formats for saved images. If the files will be staying on the Macintosh, PICT is generally a good choice, as it is readable by the widest variety of Mac software. JPEG and GIF are both popular cross platform formats for use in Windows software or in web pages. TIFF is another graphics format, which may be applicable in some contexts.

Within the different format, there are type specific options. In most cases, FlowJo only generates graphs with a small number of colors in them. But you can set a maximum, to conserve memory and conform to certain publishing constraints. PICT graphs can be created as vector based graphics, or a condensed bitmap. The axes are always created as vector based, as that improves printability and editability of the output. But creating a dot plot of tens of thousands of dots, each as its own vector definition will bring most graphics packages to their needs. Unless you plan to edit attributes of the dots (such as to emulate the "large dots" function from the Graph pane), it is best to leave this off.

GIF files can be written with a couple of fancy options, used frequently in web sites. Interlaced means that the file is written in alternating panels, so the user can get an increasingly good view of the graphic as it's being read in from the network. This is not so necessary not as it was in the days of slow modems, but is nonetheless a nice effect. Secondly, the GIF format supports having the white color to be transparent, enabling overlaying of the graph in a web page.

JPEG files use compression to save space. The degree of compression is variable, with the understanding that in most cases, increasing the compression will reduce the quality by limiting the number of colors in the image. JPEG is generally used with photographic images, so the image size and quality are critically important. In the case of FlowJo, the images are very small, use few colors and compress quite well. As a result, these settings are not going to have much effect on the output.

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