New Features report:

Licensing/Authentication 

FlowJo 11 now employs BD Access Portal (BD AP) for licensing and authentication. 

• The BD AP application is distributed with the FlowJo 11 installer download. 

• BD AP must be installed and running to allow login/authentication of FlowJo v11.  

• We highly recommend allowing/enabling update notifications for BD AP. To do this: 

  • On mac, enable notifications for BD AP through Apple’s System Settings 

  • On Windows, run the FlowJo v11 installer as an administrator, (right click on installer --> Run as Administrator), otherwise no notification. 
    
    

Performance/Memory Management 

• Various performance improvements have been implemented throughout the application.  

• Tables and lists now scroll smoothly. 

• Memory usage will grow proportionally to the size of FCS files loaded. This growth is essentially unbounded.   

  • To make effective use of FlowJo 11 Beta, load datasets that fit into the available memory on your machine. 
    
    

Workbench 

• Undo/Redo functions have been implemented, allowing the undo/redo of up to 20 previous actions. 

• Right click option in the group tree for automatic grouping of samples by keyword or staining panel. 

• Themes have been improved to show tick marks and numbers on graphs with better contrast. 

• FlowJo v11 can now be run concurrently with FlowJo v10. 
  
  

Compensation 

• The Compensation and Spectral Unmixing wizard now defaults to Spectral Unmixing with AutoSpill on.  

  • Users have options to enable: 

    • Traditional Compensation instead of Spectral Unmixing
    • Gate-based identification of positive and negative populations instead of AutoSpill.

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• Editing of a Spectral Unmixing matrix can now be performed using a square “Adjustment Matrix” where there is a 1 to 1 relationship between fluorochromes and readout channels. 

  • The Adjustment matrix is applied in addition to the existing compensation/unmixing matrix so that the original matrix is preserved. 

Graph Gallery and Gating 

• Mouseover tooltips have been added to the graph parameter axis labels to allow full view of very long parameter names. 

• Gate definitions and calculation are no longer affected by changes to transforms. 
  
  

Tables 

• Can be exported as CSV. 

• Can be added to Reports. 
  
  

Charts 

• The following Statistical Tests/Comparisons have been added: 

  • T-Test 

  • Wilcoxon rank-sum test 

• Connecting lines, asterisks representing significance and calculated p-values have been implemented as display options for the above statistical tests.

• Charts can now be added to Reports. 
  
  

Reports 

• Can be exported in PDF format. 

• Plot legends are interactive. 

  • Order of columns can be adjusted. 

  • Columns can be added to insert Keywords and/or Statistics. 

  • Column headers can be renamed. 

  • Populations in overlay plots can be designated as a Control layer, so they won't iterate when batching. 

• Charts and Tables can be added to Reports. 

• Batching by Population selection has been added. 

  • Batching by Population allows the user to select a parent population in the hierarchy and create equivalent graphs for all children of that parent in the Report Editor.  We believe this will be particularly useful for displaying cluster results. 
    
    

Preferences 

• Initial structure of Preferences has been implemented. 

  • Cytometers Preferences for setting default scaling and transformation settings. 

• Preferences can be set at three different levels: 

  • Computer 

  • User 

  • Workbench 

  • Preferences set for the computer impact all users of that computer but can be overridden for a specific user via the User preferences, which can be overwritten by that user for a specific workbench using the Workbench preferences. 

Known Issues:

• Only one FlowJo v11 workbench file can be open at a time. 

• Closing the FlowJo v11 workbench will close the application. 

• Frequencies will only be displayed as decimals and not percentages. 

• Frequencies are not currently displayed on graphs when gating. 

• Some font colors and tick marks in dark mode are too dark to see, particularly in the table editor and during text entry in the metadata manager. 

• Event # cannot currently be graphed. 

• Error toasts do not close automatically when switching workbenches. 

• All sets of quad gates on one parent population will begin with Q1, causing them to order unusually by quad number instead of grouped together by parameter. 

• Running QC on a sample w/o a time parameter produces poor results.  

• Rarely, a specific sample will produce no QC output even though it is using a plugin in version 10.10. 

• X-Shift cluster populations are not auto-gated. 

• Derived parameters derived from X-Shift do not automatically transform to the proper range to show all cluster peaks. 

• Table columns cannot be reordered. 

• Non-default table statistics ignore the hierarchy selection and must be added one at a time via the drop-down population selector. 

• The Cytometers Preferences list of available $CYT fields is currently hard coded and will not automatically add new Cytometers to this list when FCS are loaded.  

• FACSDiscover transforms encoded in FCS files take precedence over cytometer preferences, which can cause unexpected transforms on some parameters. 

• Adding a Virtually Concatenated Population (VCP) node to a Report will result in an NA plot visualization.

• Heatmap plots do not render correctly in Reports and will display with a blue background, without heatmapping.