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.

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.

Save as ACS...
Saves your workspace using XML accordance with the Advanced Cytometry Standard.

Revert
Reopens the current Workspace from disk. Any changes made since the last save operation will be lost.

Print...
Opens the Windows Print utility including Page Setup.

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.

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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.

Paste Keywords
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 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.

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.

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.

Edit Buttons...
Opens a window from which you may drag frequently used buttons into the Workspace interface.

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Workspace menu

Open Graph Window

Opens the plot or plots of any selected tubes.

Add Samples...

Add FCS files to the current Group in the Workspace.

Remove Samples...

Remove selected FCS files from the Workspace.

Add Keyword...

Adds an additional keyword to all samples 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.

Add Statistic...

Opens a window from which you may choose a statistic to be calculated on the selected populations.

Show/Hide Statistics

Hides (or shows) all statistics nodes in the workspace.

Show Frequency of Parent

Makes Frequency of Parent the default statistic in the Workspace's Statistic column.

Show Frequency of Total File

Makes Frequency of Total the default statistic in the Workspace's Statistic column.

Rename

Use this command to rename whatever item you have selected in the workspace.

Sample Properties

Opens a dialog with all the keyword information, compensation matrix, parameters and stains from the .fcs file for a selected sample.

Update Column Widths

Updates columns to best accomodate width of current data.

Export./Concatenate..

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. The Concatenate option 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.

Edit Columns...

Brings up a dialog to change the information displayed in the sample list of the workspace window.

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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...

Opens the Create Group dialog.

Edit Group

Opens the Modify Group dialog for the currently selected group.

Create Keyword Value Series

Select a cell in a keyword column. This menu item opens a dialog to set the initial keyword value, and increment it over subsequent data entries

Create Groups by Keyword Value

Select a cell in a keyword column. This menu item creates a new group including all those samples in the current group that contain the selected keyword.

Copy Gate to Group

Select a subpopulation in the Workspace. Use this menu item to copy the gate to the rest of the members of the current group.

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Tools menu

Calibration...

Launches the Calibration platform that you can use to convert between the fluorescence intensity collected on your instrument and absolute numbers of fluorophores.

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.

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.

Show In 3D...

Launch the 3D platform to create an image in x, y, and z axes.

Create Combination Gates...

Automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates.

Boolean Gates

Select a parent population, specify subpopulations upon which to apply And - Or - And not - Or not... the gated populations will appear in the Workspace list.

Windows Menu

Acquire Sample Data...

Launch the Cytek acquisition module, called Cypod. CyPod is compatible with Facscan™, Facsort™ and FacsCalibur™ flow cytometers upgraded by Cytek Development.

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 a 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.

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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.