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

• Workspace
• Graphs & Gates
• Layouts & Tables
• General

The appearance of the preferences window changed substantially with Version 3.3 (February, 2001). If these windows do not look like what you see in the program, please click here.

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 section marked 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 display 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.

You can specify the font and size of the text drawn in the workspace.

The final button in the section is to set the order and size of columns visible in the workspace. 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 right section, Behavior relates to preferences regarding the workspace operations. One options is to auto-save your work, protecting from loss of (much) data, should the program or computer crash. 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).

The popup menu for "Adding Analyses to the Workspace" controls how FlowJo causes recalculation of gates & statistics that are copied between subsets (or samples) to occur.  Depending on how large your experiment is, it may become cumbersome to have FlowJo recalculate all populations affected by the action of dragging a population to a group or sample. This setting will permit you to postpone recalculation on some or all samples to maintain the responsiveness of the program. 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 next 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, but will not change the appearance of existing graphs or graphs made on currently compensated parameters.

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).

"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.

The button at the bottom of this section, marked "Define…" goes to a separate dialog specifically for dealing with the data generated by Becton Dickinson's digital Vantage (Diva) system. This 32 bit linear data does not fit the normal data standards used by other instruments, but FlowJo has special settings to allow you to understand the acquisition files.

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Graphs & Gates Preferences

The first section is labeled Graph windows: Appearance. 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 graph type and options are identical to those you can specify in the floating graph tools window. This will be the default graph type displayed whenever you open a sample for the first time.  "Forward scatter on X...", when checked, specifies that FlowJo shows Side scatter vs. Forward scatter the first time you open a sample's data (otherwise, it shows Forward vs. Side scatter).

The font information is applied to axes 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 checkbox Use Scientific Notation for Log Axis labels with direct the program to draw axis labels as 10⁰, 10¹, 10², etc. If unchecked the labels would be drawn 1, 10, 100, etc.

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.  This can either be an absolute number, or a percentage of the total number of events in the population. If you enter 0 in this box, regardless of the radio buttons' settings, all of the events will be drawn.

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 Gating section groups preferences together that determine the behavior of gates and gated populations.  "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. "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.  "Auto-select gating tool when clicking in a graph" speeds the process of creating gates, because the mouse is automatically ready to start creating a polygon or other gate. If this is off, then you need to select the tool in the Graph Tools Window before gating. "Choose rectangle gate by default" determines whether the polygon or rectangle is the default gating tool. "Auto-set tinting for new gates" if checked will set the attribute to draw the gates with a colored tint. (Be forewarned that sometimes when exporting tinted gates, the color will become opaque and hide the data underneath the gate. Test with your presentation or graphics editing software before using tinted gates too freely.)

The set of preferences in the box marked "Graph options for new subsets" 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.

Finally, you can create a custom list of population names that you use frequently. If this list is defined, the population creation dialog will show an additional popup menu listing all of the names you have defined. This will facilitate more consistant naming conventions, and reduce redundant typing.

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Layouts & Tables Preferences

The first section Table Output View contains only options specific to the Table Editor. Tables can optionally include summary statistics as additional rows in the output tables. If this is checked, additional rows for mean and standard deviation will be appended to the table. If the summary statistics are showing, values in the table will also be highlighted. If the value is greater than one standard deviation from the mean, it will be bold and italicized. If the value is greater than two standard deviations from the mean, it is also turns red.

The option "Use 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 by substituting % for frequency, P for parent, and G for grandparent.

Within the Layout Behavior section, you can choose the default format of batch layouts. The choices include New Layout, Tiled Report, Web Report or Movie. You can learn more about the options here.

When making histogram overlays, it is sometimes useful to separate the curves so that the overlap does not confuse the graphic. This checkbox will offset successive curves in the overlay so that it is easier to read them. "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. 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.

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

The check boxes in the section Use Layout Annotation determine which information is included in the annotation of a graph added to a layout. The title, sample name, population, path, frequency and count can each be individually included in the annotation.

When HTML is produced, either directly from the layout editor, or from the tiled or animated views of the batch window, the file format of the data is controlled by these options. You can choose between the JPEG, GIF, TIFF or PICT file formats. You can also choose files that contain additional HTML for the header and footer of the pages you produce. These may contain your logo or link information that you want included in the pages you create.

"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.

The right half of the pane, containing the section Layout: Appearance has the font, size, style and color controls for the different text boxes in the layout editor.  The checkbox "Draw Border" 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.

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General Preferences

The first section of this pane General Appearance & Behavior controls miscellaneous settings that affect the program's look-and-feel. Mute Sounds will suppress the various sounds FlowJo makes when completing actions such as copying to the clipboard or adding a statistic to the workspace. Don't use 'live' window... enables a relatively new feature in Apple's operating systems. If this is checked, the system will support dragging entire images of windows, instead of the outline boxes, as older Macintosh systems supported. If you are running FlowJo on a system older than 8.5, make sure this box is clicked as the 'live windows' will crash your computer. The box to Hide Graph Tools window when it's not needed will cause the graph tools floating palette to disappear if the current window does not use the palette. Alternately, the window will remain visible, but its controls will all be deactivated.

FlowJo has a "task monitor" window, a small status bar that displays the current number of graphs and calculations it is currently working on. Because its workload can sometimes get quite extreme, the monitor window can be useful in assessing how much longer you have to wait. This popup menu will let you position or hide the Task Monitor Window.

FlowJo collaborates with other applications to simplify your workflow. You can define helper applications for three functions: displaying tabular data, displaying graphical data, and displaying help pages.

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. In response to the Help button in any of the FlowJo's windows, the program will direct the Finder to launch your chosen Browser, and display the HTML reference manual page specific for the context.

The settings within the box labeled Remote data transfer, are only used by a small number of sites that provide centralized data storage for their FCS files. If files are stored remotely, FlowJo can use FTP or HTTP to download them to your Macintosh as they are needed. To speed up subsequent access to the same files, FlowJo maintains a cache on local hard drive. These settings will determine the maximum size of the cache, and whether the program should delete all of the files when it quits.

The top right pane governs preferences on Exporting Graphics. 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 as necessary 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 the overlaying of graphs 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.

"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.

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