• Workspace
• Graphs
• Layouts
• Text Traits
• Additional Options

Workspace

Appearance

• Draw Column/Row Borders - allows you to enable or disable drawing of the lines that separate 'cells' of the workspace
• Gate Statistic is Frequency 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.
• Mute Sounds - controls wether or not FlowJo's use of auditory signals to accent certain events.
• Copy $Comment - this will place the $comment keyword into the Annotation column in the workspace
• Show Open Windows At Startup - will open a saved workspace with open graph windows

Saving Workspaces

• Remind to Save every.. - specify the interval of how often you want FlowJo to remind you to save your work
• Add incrementing version number to name - saves workspaces to a new file with an incrementing file name (workspace001, workspace002 etc..)
• Show Elapsed Time Since Last "Save"

Keywords

• Default / Use data file name / Specify Keywords - choose how you would like to identify samples in the workspace.
• Make Default - sets the order and size of columns visible in the workspace. If you click on "Make 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.

Serial Number

• Hardware Address - the main active hardware address of your computer will show here
• WiFi HW Address - the secondary or wireless adaptor of your computer will show here
• Serial Number - copy and paste your serial number into this field.
• Dont Check... - when checked, this option will not notify you of any new versions of FlowJo.
• Check...- when checked, you will be notified of new beta versions of the software.

Graphs & Gates Preferences

Attributes

• Graph type - select a default graph type from this pulldown. Different graph types are discussed here.
• Contour Levels - choose how many percent of events each line represents. The last N events can be displayed as "outliers".
• Smoothing - in certain types of plots this option will blend dots into smears of color for easier visual characterization of density.
• Show Outliers - in certain types of plots, outliers will display the least dense events as dots.
• Fore/Back/ground color - foreground color controls dots and lines in dotplots and contour plots. Background color is the blank space with no events.

Gate Appearance

• Show Gate Frequency on Plots - When enabled, this option will show %age of cells in a gate.
• Show Live Quadrant Statistics - When enabled, this option will track the chaning %ages in each quadrant as the mouse is moved when the quadrant gating tool is selected.
• Auto-Select gating tool when clicking in a graph - when enabled, this option will enable you to begin drawing a gate immediately. By default this will be the polygon gate.
• Choose Rectangle Gate by default - this modifies the previous option to use the rectangle gate instead.
• Set "tinted" for new gates - this will add a color tint for all new gates.

Options

• Forward Scatter on X Axis by default - when checked, the FSC parameter will be on the X axis
• Add Event Number Parameter to All Samples - adds an event number to all events in all samples
• Use Scientific Notation for Log Axis Labels - will use 10^2 instead of 100
• Number/Percent of dots drawn - you can either type in a percentage or number of dots to be displayed in your Dot Plot graphs. This setting does not affect anything but Dot Plots.
• Draw Large Dots (outliers & dotplots) - this setting, when checked, will draw dots that are large.

Child Populations

• Display other parameters..- when this option is checked, double-clicking a gate in a Graph Window will open another graph window with different parameters displayed than the original.
• Show child graph..-allows you to control how the child graphs should be displayed.
• define std pop names..-enter your favorite population names here. They will be available from the population name dialog that pops up any time you draw a gate.
  

Layouts & Tables Preferences

Layout Options

• Batch Format - currently only New Layout is functional.
• Allow Stain Name Mismatch - if checked, the batching will ignore stain name differences
• Offset Histogram Overlays - if checked, all new histogram overlays will be offset.
• Use Placeholders - if checked, will draw a placeholder in place of graphs to reduce calculation overhead.
• Enable Auto Select - if checked, mouse cursor will select objects underneath it as it moves over them.
• Fore/Background - pick the colors for your fore/back/ground.

Use Layout Annotations - when checked, the below options will take into affect:

• Show Graph Title - will show a box with the title, ex. "Pseudocolor Plot of SSC-H vs. FSC-H"
• Show Population Name - will show a box with the population name, ex "Lymphocytes"
• Show Sample Name - will show the sample name keyword value
• Show Full Path - will show all the parent nodes of the displayed node, ex. "Lymphocytes:CD3+"
• Show Frequency - will show freq. relative to the total events in the file
• Show Count - will show how many events in the current graph

Extras

• Draw Borders around Text Boxes - will draw boxes around text boxes ;)
• Save Graphis as.. - select which output format you like for your graphics. We recommend PNG for bitmap and SVG for vector.
• Show Grid Layout At Startup -
• Enable Snap to Grid At Startup - will snap all objects in the layout to the dimentions of the grid
• Choose a custom grid size - 16 is default
• Define Legend Palette - select the first 12 colors for overlays here
• Headers and Footers.. - define your header/footer info here

Text

The Text tab in FlowJo preferences allows customization of text in various parts of FlowJo. Please choose the Function, then adjust the text settings and examine the changes. You can click "use for all" button to apply a certain font/size to all Functions.

Additional Options

Email Options

• outgoing address - we recommend leaving this default, otherwise we may not get your email ;)
• your address - if you would like us to write you back, type in your email address here. We will not send you spam. We will not sell your email address to spammers.
• email probs to flowjo - if problems happen, they will be emailed to Tree Star.

DiVa Options

• transform comp'd data - this will transform all compensated data, DiVa or not.
• neg/pos logs - define the range of your biexponential axes. We recommend 2 for negative and 4.5 for positive.
• define diva data parameters - more specific options for the Diva Settings:

Default Program Options

• Choose online help browser
• Choose default bitmap program
• Choose default vector program
• Choose Spreadsheet program