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10.09 FlowJo Integration

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Note: Unfortunately, the integration with LabArchives is not available with the latest versions of FlowJo 

FlowJo flow cytometry software (from Treestar) includes the ability to do the following: 

  • Save FlowJo workspaces directly into LabArchives Notebooks 
  • Open FlowJo workspaces from your LabArchives Notebooks 
  • Retrieve samples (e.g. FCS files) from your LabArchives Notebooks into a FlowJo workspace. 

The FlowJo integration is included in version 7.6.3 and higher for PC, and version 10 for Mac. 

To activate this function, you must first go to Edit–>Preferences, and then double-click on the Licenses icon. There, you will see a small section on LabArchives which you must “Configure”.  Put in the LA server (defaults to which is correct unless you have a local server option) and your user name and password. For users in Australia, use

If you login using a Single Sign on system you will need to create a password token. For more information Click Here.

Once activated, there are two new options on the File menu: 
Save As Remote (this enable you to choose a Notebook, Folder, and Page into which to store your FlowJo Project) 
Open Remote Workspace (enables you to open a workspace stored in LabArchives) 

In addition, there will also be an icon for retrieving samples on the main screen:  

Click on this button to load a sample file from your LabArchives Notebook. 


FlowJo for Mac

Connect FlowJo to Your LabArchives Account 

1. In FlowJo, click the blue heart to open Preferences.

2. In Preferences Select “File Formats” (shown below). 

3. In the File Formats window type in your username into the LabArchives section and click “OK”. 

How to Save FlowJo Files to your LabArchives Notebook 

1. To save a wsp file to LabArchives , click on “Save.”

2. In the “Available Repositories” window, choose “LabArchives”, then click “OK”. 

3. Once LabArchives has been selected, a new work space will open showing the contents of your notebook.  After selecting a location in your notebook, the FlowJo file will be uploaded.  

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