Released 5.29.2026
Version 11.2 is a release centered around adding the Cluster Explorer and addressing customer requests for algorithms and histogram controls.
Features
Cluster Explorer - A new context has been added to FlowJo v11 that allows users to visualize clustering results in a fast and flexible manner. The Cluster Explorer includes:
A color coded 2D overlay of all child populations of a selected parent, thus allowing the user the flexibility compare clusters alongside manually drawn gates. The overlay will automatically select dimensionality reduced parameters if present, but can be changed by the user.
A bar chart comparing population sizes
A line chart showing cluster median expression for all selected parameters allowing the user to understand what kind of cells might comprise each cluster and how the expression intensity compares to other clusters
A heat map also showing median intensity of all selected parameters for all clusters. Selecting a row in the heat map also highlights that cluster across all plots.
Histogram overlay controls in Reports - Normalization and offsets have been added to histogram overlays in reports.
Normalization options include unit area, modal, and manual providing options for comparing data
Offsets have been implemented using a slider that allows the user to stack their histograms with whatever separation they prefer within the bounds of the graph size.
Opacity can be controlled via slider on the color selector.
FlowSOM - A popular clustering algorithm developed by Sophie Van Gassen while in the Saeys lab at the VIB in Belgium, has been added to the platform list, giving users a choice of clustering tools. FlowSOM is a two step algorithm that uses a Self Organizing Map to model the data as a series of nodes, and then a second step to cluster the nodes.
UMAP - Uniform Manifold Approximation and Projection is a popular dimensionality reduction algorithm developed by Leland McInnes, that allows users to represent high-dimensional data on a low-dimensional plot. UMAP provides an option to tSNE that improves preservation of the global structure of the data.
Image sets - Image sets are a new tool in the Image Wall that allow users to hand-curate a set of particularly interesting images. The selection of an image for an Image Set automatically adds the cell to a new population in the hierarchy, allowing users to make a more concise set of images and refine their gates non-linearly, while setting the stage for more sophisticated image analysis that requires training data.
BD Access Portal - Combined with an update to BD AP 2.7, FlowJo will now start BD AP for you if its on your computer, so you no longer need to remember to start both. Additionally, the start up screen includes a Sign In button if needed, and a link to the help documents. Lastly, the login window includes diagnostic tools now that can be used to troubleshoot.
Improvements
Analysis Hierarchy and Graphs
- Frequency of parent added as a default hierarchy option
- Which parameter to display when selecting a population improved
- Location of default gate name is offset
Meta Data Manager
- 'Enter' on the keyboard will advance to the next row in the keyword tab
Unmixing
- Correction matrix from Chorus handled
- Percent vs. Ratio option included so user can control normalization
- AF extraction workflow simplified
- Unmixing matrices have an expanded color palette.
Tables
- Columns can be renamed with custom value
- Sorting Improved
Reports
- Undo action improved
- Modifications in Primary Plot linked to Reports
- Report legends improved
- Columns can be renamed in tables and the legend
Image Analysis
- The image analysis tools now include the ability to save multiple filter sets and apply them to a sample with a single click.
General
- Improved handling of Sony data
Limitations and High Priority Issues
Authentication
- BD Access Portal can be blocked by security software, Z-scaler and Crowd Strike in particular.
Quality Control
- Parameter selector does not yet have a parameter set filter
Analysis Hierarchy and Graphs
- The Active Gate selection in the Graph Gallery shows the parameters of the parent population and cannot be adjusted. Work Around: Use View Target Population.
- The properties panel parameter selector will allow you to pick a parameter set without selecting a parameter, leading to the possibility of using a parameter not in the current set.
- Heat map statistics plots do not work on the Good Events population created by QC, it just produces a blue plot.
Image Analysis
- Right-clicking an image set from the analysis hierarchy and choosing Copy Image Set will only paste text. Work Around: Right-click on the images of an image set and make the same selection. It will paste images.
Tables
- Columns cannot be re-ordered by drag and drop.
Reports
- Histogram offsets cannot yet be staggered to create a pseudo-3D view.
General
- Long running algorithms can dominate computer resources, making it difficult to run additional programs while calculating.