FlowJo Menus
This is a picture of the main menu in FlowJo for Windows. Click on a menu item below to read about each of the choices in the menu.
File Menu
New Workspace
Opens a new, empty workspace.
Open Workspace
Open an existing workspace. Use the Open Workspace dialog to select a workspace that you have previously saved.
Open Recent Workspace...
Displays a list of the 10 most recently saved .wsp files. Click on one to reopen it.
Open Workspace in New Window
Opens a saved Workspace without closing the current one.
Save
Saves the current contents of FlowJo including tables, layouts and analyses as a .wsp file. If it has not been saved before, FlowJo will ask you to name the .wsp file.
Save as...
Saves a Workspace with a new name.
Save as Template...
Saves the Workspace and analyses but without data files. You can open a template and add new data. If identically stained, it will be arranged in the same groups and gated with the same gates as the data from which the template was made.
Revert
Reopens the current Workspace from disk. Any changes made since the last save operation will be lost.
Page Setup...
As in most Windows programs, this item opens the Page Setup Dialog to prepare the page for print
Print Preview...
Displays a preview of the page you are about to print.
Print...
Opens the Windows Print utility.
Close Workspace
Exits FlowJo. If you have made changes to the Workspace, FlowJo will ask if you wish to save those changes.
Exit
Exits FlowJo. If you have made changes to the Workspace, FlowJo will ask if you wish to save those changes.
Edit Menu
Undo
Cancels the last operation
Redo
Reinstates a cancelled operation
Cut
Removes selected text or items and places them on the clipboard.
Copy
Copies selected items to the clipboard
Paste
Inserts the contents of the clipboard into the active selection.
Clear
Removes selected text or items and places them on the clipboard.
Select All
Select all items in the current window.
Select None
Deselects any existing selection in the Workspace.
Select Every
When you mouse over Select Every the menu on the right appears. You can select every other, third, fourth, fifth sample etc. based on the value chosen from the popup menu. This can be useful with regular protocols where, for example, every fourth tube is stained with the same reagent. Being able to select by interval is convenient for dragging several regularly spaced samples to a group.
Select Equivalent Nodes
Selects all data entries that occupy the same place in the gating hierarchy. This way you can quickly select, for example, all of the CD4 gates for all samples.
Open Graph Window
Opens the graph of the selected population or populations. Same as double-clicking a population name in the Workspace.
Collapse All
Collapses the subset display in the Workspace so that only the imported tubes and their disclosure triangles are visible.
Expand All
Displays the complete hierarchical analysis structure with gated populations, statistics, and other analyses displayed.
Collapse Level
Select a population or subset. Collapse Level will close the analysis hierarchy below the selected level on that item. To reopen it select Expand Level, or click the disclosure triangle next to the item of interest.
Expand Level
Reveals any hidden items in the analysis hierarchy. Equivalent to clicking the disclosure triangle next to a hidden analysis hierarchy.
Text Traits...
Opens a dialog within which you may set the font name and size.
Preferences...
Opens a dialog to set your personal preferences for sample naming, decimal precision, default gate statistic, serial number and others. CLICK HERE for the full rundown.
Save State to Preferences...
After configuring open windows to your liking, choose this option. It will record the current state of the window as the default. The next time you open the window, your preferences will prevail.
Workspace menu
Show Workspace
Brings the workspace window to the front.
Show/Hide Statistics
Hides (or shows) all statistics nodes in the workspace.
Edit Workspace Columns...
Brings up a dialog to change the information displayed in the sample list of the workspace window.
Sort Sample List...
Brings up a dialog that lets you sort the sample list by a variety of keys.
Add Keyword...
Adds an additional keyword to the sample's record in the workspace, for additional annotation. Note that this does not alter the FCS file, but only creates the keyword within the scope of the current workspace. To permanently and universally add the keyword, you should use ProJo.
Copy Value to Group/Create Value Series
This takes the value in the currently selected field, and applies it to all of the samples in the current group. This is useful for creating keywords with a value shared by all of the members of a group. When you select a keyword and hold down the Option key, you see Create Value Series. A dialog lets you set the initial keyword value, and increment it over subsequent data entries.
Make Groups From Keys... /Groups From All Values
Opens a dialog to choose a keyword as the basis for a new Workspace group. You can give the new group its own color and text style here too. Option key lets you make a group or groups that share a single value of a keyword.
Add Samples / Add Samples Into Group
Add FCS files to the current workspace. Option key lets you select a group and import new samples to it.
Add Samples From Network
Enter a URL and import samples from elsewhere.
New Group... /Put into new Group
Create a new grouping of samples. Brings up the Group Definition dialog. If you first select some samples you want to group then hold down the Option key, Put into new Group creates a group of those samples. The same results from the keyboard command Option-command-G.
Recalculate / Clear & Recalculate
This command asks FlowJo to compute all statistics and frequencies for the populations that are selected. In addition, all descendants of selected populations will also be recalculated. Clear & Recalculate Forces FlowJo to recompute all statistics for all populations, whether or not they have previously been computed. Keyboard equivalent is Option-command-=
Unify Analyses
If you have modified a gate and decide later that it should be identical to the group's version, you can select the gate and choose the Unify Analyses option. Likewise, if you select a group then choose a gated population within it, you can use Unify Analyses to apply this GROUP version of the gate to any samples whose gates have been changed. Learn more about groups.
Rename
Use this command to rename whatever item you have selected in the workspace.
Get Sample Info
Opens a dialog with all the keyword information, compensation matrix, parameters and stains from the .fcs file for a selected sample.
Export...
Export the data from one or more samples and gates as .fcs files or chose to export channel or scale values as an ascii (text) file. Learn more about exporting raw data.
Concatenate Samples
Combines the data from multiple samples into a single sample and saves it to disk as a .fcs file with the name of your choice.
Groups menu
Copy Value to Group
This takes the value in the currently selected field, and applies it to all of the samples in the current group. This is useful for creating keywords with a value shared by all of the members of a group.
New Group...
Create a new grouping of samples. Brings up the Group Definition dialog.
Create Value Series
When you select a keyword and click Create Value Series, a dialog lets you set the initial keyword value, and increment it over subsequent data entries.
Create Groups By Keyword Value
Opens a dialog to choose a keyword as the basis for a new Workspace group. You can give the new group its own color and text style here too. Option key lets you make a group or groups that share a single value of a keyword.
Tools menu
Cell Cycle Platform
Launch the Cell Cycle Platform to perform DNA analyses.
Kinetics Platform
Launch the Kinetics Platform to perform time-dependent analyses.
Proliferation Platform
Launch the Proliferation platform used in conjunction with cellular markers to study the rate of cell replication.
Derived Parameters...
Derive new computed parameters or copy the derived parameters from a sample to other samples. You can only add derived parameters to a single sample; you can only copy derived parameters from a single sample that has them defined. From this menu item you can also delete unwanted derived parameters.
Compensation Platform
Define or apply a compensation matrix. This menu item has a submenu of Compensation processes. If a group is currently selected, then all samples in that group are compensated; if a sample is selected, only that sample is compensated.
Calibration...
Launches the Calibration platform that you can use to convert between the fluorescence intensity collected on your instrument and absolute numbers of fluorophores.
Create Background Gate...
Boolean Gates...
Select a parent population, specify subpopulations upon which to apply And - Or - And not - Or not... the gated populations appear in the Workspace list.
Windows Menu
Layout Editor...
Define or create a new layout for graphics presentation. Brings up the Layout Editor dialog window
Table Editor...
Define or create a new table of statistics. Brings up the Table Editor dialog window.
Compensation Editor...
Define or apply a compensation matrix. This menu item has a submenu of Compensation processes. If a group is currently selected, then all samples in that group are compensated; if a sample is selected, only that sample is compensated.
Plate Editor...
The Plate Editor is a 96 well plate editor for describing staining setup using attribute - value pairs. The Plate Editor enables creation and editing of samples prior to collection, or as a way to edit sample descriptions after collection.
Help Menu
About FlowJo
Shows which version of FlowJo is running.
Release Notes
Shows a file of the most recent changes to the current version.
The Daily Dongle
Launches a web browser to the FlowJo blog.
FlowJo Reference Manual
Launches a web browser with the main help pages.
FlowJo Tutorials
Launches a web browser with links to download our tutorials.
FlowJo Demo Data
Launches a web browser with data sets which can be read into FlowJo when it is running in "Demonstration Mode"--the free, fully-functional analysis mode, for which the only limitation is the ability to read only the data files provided by Tree Star, Inc.
Help with Workspaces
Launches a web browser with a Workspace Overview.
Adding Samples
Launches a web browser describing how to add samples.
About Groups
Launches a web browser describing group attributes.
Using Statistics
Launches a web browser with an overview of FlowJo Statistics.
Check for New Version
Launches a web browser with a link to the latest version download.
Installation Help
Launches a dialog box with FlowJo License Information, including hardware address and serial number.
Report Bug
Launches a web browser with a bug report form.
Contact FlowJo Support
Launches an email form for contacting Technical Support.
Save as Archive
Opens a dialog box to save the file as a .zip file.
