Archive Files


The Archive file type (acs) is a convenient way of grouping the fcs files with their analysis. Saving the FlowJo Workspace as an archive files will create a large file that contains the workspace its associated data files and its plugin derived parameter files. A file can be saved as an archive file by selecting… Read more »

Batch Using Iterate by Keyword


For many types of batch reports, simply iterating by the Sample or Panel are the easiest option, but in some cases we need to be more specific about which samples to include in the batch reports. In this case we can use iterate by keyword. Iteration by keyword uses a pair of keywords to specify… Read more »


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Introduction PhenoGraph is a clustering algorithm that robustly partitions high-parameter single-cell data into phenotypically distinct subpopulations. First, it constructs a nearest-neighbor graph to capture the phenotypic relatedness of high-dimensional data points and then it applies the Louvain graph partition algorithm to dissect the nearest-neighbor graph into phenotypically coherent subpopulations. The PhenoGraph algorithm has been implemented… Read more »

Sample Quality Check


The Sample Quality Badge can be used to simply access the quality of each of the samples using the metric discussed in Sample Properties. This check can be performed by simply double clicking on the circle to the left of the file name. The color of the dot will indicate the relative quality of the… Read more »

AutoSpill Compensation


AutoSpill is a new algorithm for calculating spillover and producing a compensation matrix developed and incorporated into FlowJo v10.7 in collaboration with researchers from the Vlaams Instituut voor Biotechnologie in Belgium and the the Babraham Institute in Cambridge, UK. This form of gate-less compensation removes some of the requirements of traditional compensation making compensation faster and simpler…. Read more »

10.6.2 Exhaustive Release Notes


Updates Functional within Mac OS 10.15 (Catalina) – Requests permissions to access files and folders Update to use Java version 9 Increased absolute value of negative option for scaling in BiExponential Include No More Than option in Export/Concatenate menu is being updated for full functionality Open Original Graph option from the Layout Editor now opens… Read more »

10.6.2 Release Notes


New Features: Fix issues in Mac OS 10.15 (Catalina) Update to use Java version 9 Improved support for JO workspace reading Performance enhancing features Multigraph overlaid plots in the Layout Editor now allow for additional plot type customizations More Info For more about features and a list of known issues, see the exhaustive release notes.

Dimensionality Reduction


Visualize all of your parameters in a single 2D approximation! Dimensionality Reduction has become a popular way of visualizing high parameter datasets. Most of the dimensionality reduction algorithms for FlowJo are available as plugins on FlowJo Exchange, hosting these tools in plugin form allows for very rapid deployment and development. The tSNE algorithm has been… Read more »

Plugin Demonstration Videos


Plugins add a wealth of features to FlowJo adding on to its analysis base. These plugins can be downloaded from the FlowJo Exchange on our website. The FlowJo plugins are constantly being updated with new tools designed by the research community, allowing users to stay on the cutting edge of analysis. Each plugin has a… Read more »

So You Want to Become a Plugin Developer?


That’s awesome! You inspire us… We encourage aspiring bioinformaticians and researchers with a knack for computer science to create their own plugins using the APIs available in FlowJo applications. You can find the latest update to our developer guide here: As you have questions, or if you’d like to collaborate on your plugin development… Read more »