• Spectral Plots: Create spectral plots for selected detectors and populations
• Spectral Population Viewer: Compare populations using spectral plots
• BD SpectralFX™ Technology Unmixing: Perform system-aware spectral unmixing on spectral data from BD FACSDiscover™ S8 Cell Sorters
• Advanced Scaling Preferences: Define data-driven, per cytometer scaling to more easily set transform properties
• Cluster Explorer: Explore added functionality
  • Non-cluster populations can now be visualized in the cluster explorer
  • Clusters can be re-ordered within the heat map view
  • Heatmap columns can be re-ordered or hidden
  • Expanded heat map window
• Table creation for MEM scores: Export MEM population names in a tabular format
• Copy Transforms: In the compensation matrix editor users can now copy the transform from one compensation matrix to another, allowing per parameter transforms to be easily applied to another data set
• Hyperfinder: Define populations identified by a computational approach with standard gates so that they might be sorted
• NxN plot parameter mouseover: Display parameter combinations on NxN plots for easier viewing

• Embed: Forward propagate clustering or dimensionality reduction results to new files with the same parameters.
• Autofluorescence extraction in traditional (gate-based) compensation: Use an unstained cell data file and true zero as the background value to model autofluorescence for extraction.
• MEM – Marker Enrichment Modeling (MEM): Re-name clusters automatically and quantitatively based on their marker expression with a human- and machine-readable label.
• Spectral similarity scores: Calculate the cosine index for acquired data to evaluate reagent choices made in panel design based on data from your specific instrument and experimental conditions.
• Auto-Quad gates: Automatically create quads and rectangle gates based on range gates, bi-sector gates or the data itself.
• Clone gates: Gates with the same name can now be linked together as ‘clones’ so that their position is synchronized.
• Native Cluster Explorer: Display line charts, bar charts, heat maps, and dimensionality reduction plots of clustered data in FlowJo without the use of a plugin.
• Improved interactions with BD® Research Cloud: Save and load options throughout the software now include the BD® Research Cloud as an option.

New Features:

• Support added for FCS files greater than 3 GB
• Improved support of MQD files
• Improved support for non-BD cytometer acquired data. 
• Built-in tSNE improved to produce better optimized plots, addressing issue introduced in 10.7.2. We have corrected an optimization issue so that the outputs produce better defined islands.
• Improved support for bulk conversion of Jo Files

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• Improved calculation speed on large workspaces.
• Spectral compensation matrix normalization aligned with spectral compensation in BD FACSDiva™ Software
• Added functionality in direct opening of .jo files
• Improvements to FlowJo Portal sign in

More Info

For more about features and a list of known issues, see the exhaustive release notes.

• Improved authentication. The HTTPS connections to FlowJo Portal for authentication/authorization purposes can be secured by either a FlowJo SSL certificate or newly by an SSL certificate installed by the end user’s corporate security or IT.
• Total Spread Matrix (TSM) is now available for matrices created in FlowJo. TSM is the Spillover Spreading Matrix (SSM) without normalization to the florescent intensity of the probe. Panel designers consider the brightness of a dye as well as its spread as factors impacting that ability to separate populations. These factors are combined in the SSM metric, but de-coupled in TSM so that the designer may factor in the total spread introduced into a panel apart from brightness. This new measure is available in the SSM dropdown in the Compensation Editor.

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• New AutoSpill calculation available in the Compensation Wizard. This novel feature allows researchers to compensate datasets without the use of negative and positive gating. The algorithm published by Roca et al. (doi.org/10.1101/2020.06.29.177196) works by performing a regression across single stained control samples and parameters of interest to achieve even better (more accurate) compensation.
• Action Logs stored on a researcher’s local machine will now include “UserName” meta-data when logged into FlowJo from the FlowJo Portal licensing system. This supports better auditability of analyses, an important consideration for FlowJo users in controlled environments.
• For more about features and a list of known issues, see the exhaustive release notes.

New updates include:

• Compatibility with macOS Catalina 
• Improved processing speed for high dimensional data 
• Improved support for BD FACSDiva™ experiment import/export 
• Improvements to the Layout Editor, including new multigraph overlay plots and the ability to multi-select plots and simultaneously edit 
• Update to Java version 9

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

• Dongles now authenticate FlowJo with other USB devices attached concurrently.
• Parameter short name ($P#S) keywords now utilized in more locations, such as Multi-Graph Color Maps. This change replaces many instances of the less informative parameter name ($P#N) keywords.
• Changes to multi-selected plots in the Layout Editor now apply to all plots selected.
• Appropriate default scaling for BioRad ZE5 cytometers enabled.

• Spectral compensation allows users who collect more channels than they have parameters to get cleaner data if properly done. In spectral flow, light is collected in all detectors for all parameters and the additional information allows software to separate out the individual colors more precisely.
• Platform overlays unlock the ability to overlay kinetic, proliferation and cell-cycle plots from one sample onto another or multiple samples.
• Auto-Save workspace feature - new preference setting allows researchers to automatically save their analysis at a customizable time interval.
• BD and FlowJo continue to support you and your research, from design to discovery. Now with the new FACSDiva™ support, users can import and export gates and compensation directly to a FACSDiva™ experiment.
• For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

• New native tSNE Platform now offers super high performance dimensionality reduction. 
• Bug fixes

For more about features and a list of known issues, see the exhaustive release notes.

• New native implementation of t-SNE; this is several times faster than the original plugin implementation and thus it scales better to larger inputs. (For backwards compatibility, the plugin-based t-SNE is still available)
• Improved memory management.

For more details on features in this release, and a comprehensive list of known issues visit  
the exhaustive release notes.

• FlowJo Portal Authentication
• Includes a new and enhanced computing engine, for improved performance.
• Drag and drop merging of CSV parameters into data matrices now supported.
• FlowJo is now fully GDPR compliant.
  
  For more details on features in this release, and a comprehensive list of known issues visit 
  the exhaustive release notes.

New Features

• FlowJo icons on high resolution monitors now correctly sized.
• FACSLyric data now gets its own badge in FlowJo’s Cytometers preferences, and utilizes standard BD transformations by default.

Bugs Fixed

• Fixed incorrect statistics reported for some MQD data files.
• Downsample populations no longer dropped from ACS files.
• $PnE keyword value no longer altered during export.

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

New Features

• Search bar added to parameter selectors in the graph window.
• Color mapped (aka “heat map statistic”) parameter labeling in layouts.

Bugs Fixed

• Proliferation Platform Improvements
• Stopped Compensation Wizard matrix re-calculations (ad infinitum).

More Info

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

New Features:

• FlowJo Envoy integration now allows for seamless access to data in FlowJo Envoy workflows.
• Hotly anticipated color mapping within the graph window, to illustrate a third parameter there is now available.
• Signal spreading matrix (SSM) now available in the Compensation Editor.

Bugs Fixed:

• Keywords now import into text-boxes in the Layout Editor.

Warnings:

• When saving an ACS file from an FlowJo Envoy based workspace, the default location prompt is a temporary cache folder, which will be deleted when FlowJo is closed!
  • Workaround: Save FlowJo Envoy based workspace ACS files to a known, stable local directory.

More Info

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• We are happy to announce that the Proliferation Platform is here!
• We have revised the Logicle Transform implementation. Existing workspaces with gates using this transform may need to be adjusted.

Warnings:

Because FlowJo® now uses Java 8, we no longer support Mac OS 10.6.8 (because it does not support Java 8).

Major Changes:

• Proliferation Platform: FlowJo now supports Proliferation.
• Revised Logicle Transform implementation to synchronize the user interface and the correct display ranges.
• Java 8: FlowJo now uses Java 8, which brings a number of security and reliability improvements. This capability is now is distributed with the FlowJo install on both Windows and Mac.
• Mac OS Sierra (10.12): This OS is now fully supported.

Note: This version of FlowJo is compatible with FlowJo Enterprise v2.0 or the newly released FlowJo Enterprise 2.1. Be sure your version of FlowJo Enterprise is new enough before installing this version of FlowJo.

FlowJo can now use plugins that can perform a variety of functions, including the creation of populations, creation of derived parameters, and actions when opening or saving a workspace. 

The open plugin architecture of 10.2 allows access to cutting edge tools that can be integrated into your current analysis workflows, and we will be releasing developer documentation so any tool can be integrated into FlowJo. FlowJo 10.2 includes a set of tools for discovery including downsampling, tSNE and CellOntology. You'll find these as 'plugins' in the populations band -- each offers one-click access to powerful tools to reduce any number of parameters to two and to query a database to name unknown populations.

New Features:

•Increased the number of parameters that FlowJo can analyze to 1000

•Added a field to allow specification of R's path in prefs (Diagnostic Panel)

•Better interface for Licensing Preferences Panel in the case where a computer has many hardware addresses.

•Updated EULA to raise the awareness of the fact that you may not install FlowJo on a VM.

•Unchecked 'Display other X/Y parameters than in parent plot' as default in Gates Preferences

•Removed the option to downsample when concatenating files. (Downsample before you concatenate if desired.)

Full Release Notes

• Spectral Plots: Create spectral plots for selected detectors and populations
• Spectral Population Viewer: Compare populations using spectral plots
• BD SpectralFX™ Technology Unmixing: Perform system-aware spectral unmixing on spectral data from BD FACSDiscover™ S8 Cell Sorters
• Advanced Scaling Preferences: Define data-driven, per cytometer scaling to more easily set transform properties
• Cluster Explorer: Explore added functionality
  • Non-cluster populations can now be visualized in the cluster explorer
  • Clusters can be re-ordered within the heat map view
  • Heatmap columns can be re-ordered or hidden
  • Expanded heat map window
• Table creation for MEM scores: Export MEM population names in a tabular format
• Copy Transforms: In the compensation matrix editor users can now copy the transform from one compensation matrix to another, allowing per parameter transforms to be easily applied to another data set
• Hyperfinder: Define populations identified by a computational approach with standard gates so that they might be sorted
• NxN plot parameter mouseover: Display parameter combinations on NxN plots for easier viewing

• Embed: Forward propagate clustering or dimensionality reduction results to new files with the same parameters.
• Autofluorescence extraction in traditional (gate-based) compensation: Use an unstained cell data file and true zero as the background value to model autofluorescence for extraction.
• MEM – Marker Enrichment Modeling (MEM): Re-name clusters automatically and quantitatively based on their marker expression with a human- and machine-readable label.
• Spectral similarity scores: Calculate the cosine index for acquired data to evaluate reagent choices made in panel design based on data from your specific instrument and experimental conditions.
• Auto-Quad gates: Automatically create quads and rectangle gates based on range gates, bi-sector gates or the data itself.
• Clone gates: Gates with the same name can now be linked together as ‘clones’ so that their position is synchronized.
• Native Cluster Explorer: Display line charts, bar charts, heat maps, and dimensionality reduction plots of clustered data in FlowJo without the use of a plugin.
• Improved interactions with BD® Research Cloud: Save and load options throughout the software now include the BD® Research Cloud as an option.

Support added for dongle authentication on Mac OS Ventura

New Features:

• Support added for FCS files greater than 3 GB
• Improved support of MQD files
• Improved support for non-BD cytometer acquired data. 
• Built-in tSNE improved to produce better optimized plots, addressing issue introduced in 10.7.2. We have corrected an optimization issue so that the outputs produce better defined islands.
• Improved support for bulk conversion of Jo Files

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• Improved calculation speed on large workspaces.
• Spectral compensation matrix normalization aligned with spectral compensation in BD FACSDiva™ Software
• Added functionality in direct opening of .jo files
• Improvements to FlowJo Portal sign in

More Info

For more about features and a list of known issues, see the exhaustive release notes.

• Improved authentication. The HTTPS connections to FlowJo Portal for authentication/authorization purposes can be secured by either a FlowJo SSL certificate or newly by an SSL certificate installed by the end user’s corporate security or IT.
• Total Spread Matrix (TSM) is now available for matrices created in FlowJo. TSM is the Spillover Spreading Matrix (SSM) without normalization to the florescent intensity of the probe. Panel designers consider the brightness of a dye as well as its spread as factors impacting that ability to separate populations. These factors are combined in the SSM metric, but de-coupled in TSM so that the designer may factor in the total spread introduced into a panel apart from brightness. This new measure is available in the SSM dropdown in the Compensation Editor.

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• New AutoSpill calculation available in the Compensation Wizard. This novel feature allows researchers to compensate datasets without the use of negative and positive gating. The algorithm published by Roca et al. (doi.org/10.1101/2020.06.29.177196) works by performing a regression across single stained control samples and parameters of interest to achieve even better (more accurate) compensation.
• Action Logs stored on a researcher’s local machine will now include “UserName” meta-data when logged into FlowJo from the FlowJo Portal licensing system. This supports better auditability of analyses, an important consideration for FlowJo users in controlled environments.
• For more about features and a list of known issues, see the exhaustive release notes.

New updates include:

• Compatibility with macOS Catalina 
• Improved processing speed for high dimensional data 
• Improved support for BD FACSDiva™ experiment import/export 
• Improvements to the Layout Editor, including new multigraph overlay plots and the ability to multi-select plots and simultaneously edit 
• Update to Java version 9

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

• Dongles now authenticate FlowJo with other USB devices attached concurrently.
• Parameter short name ($P#S) keywords now utilized in more locations, such as Multi-Graph Color Maps. This change replaces many instances of the less informative parameter name ($P#N) keywords.
• Changes to multi-selected plots in the Layout Editor now apply to all plots selected.
• Appropriate default scaling for BioRad ZE5 cytometers enabled.

• Spectral compensation allows users who collect more channels than they have parameters to get cleaner data if properly done. In spectral flow, light is collected in all detectors for all parameters and the additional information allows software to separate out the individual colors more precisely.
• Platform overlays unlock the ability to overlay kinetic, proliferation and cell-cycle plots from one sample onto another or multiple samples.
• Auto-Save workspace feature - new preference setting allows researchers to automatically save their analysis at a customizable time interval.
• BD and FlowJo continue to support you and your research, from design to discovery. Now with the new FACSDiva™ support, users can import and export gates and compensation directly to a FACSDiva™ experiment.
• For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

• New native tSNE Platform now offers super high performance dimensionality reduction. 
• Bug fixes

For more about features and a list of known issues, see the exhaustive release notes.

• New native implementation of t-SNE; this is several times faster than the original plugin implementation and thus it scales better to larger inputs. (For backwards compatibility, the plugin-based t-SNE is still available)
• Improved memory management.

For more details on features in this release, and a comprehensive list of known issues visit  
the exhaustive release notes.

• FlowJo Portal Authentication
• Includes a new and enhanced computing engine, for improved performance.
• Drag and drop merging of CSV parameters into data matrices now supported.
• FlowJo is now fully GDPR compliant.
  
  For more details on features in this release, and a comprehensive list of known issues visit
  the exhaustive release notes.

New Features

• FlowJo icons on high resolution monitors are now correctly sized.
• FACSLyric data now gets its own badge in FlowJo’s cytometer preferences and utilizes standard BD transformations by default.

Bugs Fixed

• Fixed incorrect statistics reported for some MQD data files.
• Downsample populations no longer dropped from ACS files.
• $PnE keyword value no longer altered during export.

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

New Features

• Search bar added to parameter selectors in the graph window.
• Color mapped (aka “heat map statistic”) parameter labeling in layouts.

Bugs Fixed

• Proliferation Platform Improvements
• Stopped Compensation Wizard matrix re-calculations (ad infinitum).

More Info

For more details on features in this release, and a comprehensive list of known issues visit the exhaustive release notes.

New Features:

• FlowJo Envoy integration now allows for seamless access to data in FlowJo Envoy workflows.
• Hotly anticipated color mapping within the graph window, to illustrate a third parameter there is now available.
• Signal spreading matrix (SSM) now available in the Compensation Editor.

Bugs Fixed:

• Keywords now import into text-boxes in the Layout Editor.

Warnings:

• When saving an ACS file from an FlowJo Envoy based workspace, the default location prompt is a temporary cache folder, which will be deleted when FlowJo is closed!
  • Workaround: Save FlowJo Envoy based workspace ACS files to a known, stable local directory.

More Info

For more about features and a list of known issues, see the exhaustive release notes.

New Features:

• We are happy to announce that the Proliferation Platform is here!
• We have revised the Logicle Transform implementation. Existing workspaces with gates using this transform may need to be adjusted.

Warnings:

Because FlowJo® now uses Java 8, we no longer support Mac OS 10.6.8 (since it does not support Java 8).

Major Changes:

• Proliferation Platform: FlowJo now supports Proliferation.
• Revised Logicle Transform implementation to synchronize the user interface and the correct display ranges.
• Java 8: FlowJo now uses Java 8, which brings a number of security and reliability improvements. This capability is now is distributed with the FlowJo install on both Windows and Mac.
• Mac OS Sierra (10.12): This OS is now fully supported.

Note: This version of FlowJo is compatible with FlowJo Enterprise v2.0 or the newly released FlowJo Enterprise 2.1. Be sure your version of FlowJo Enterprise is new enough before installing this version of FlowJo.

Sierra, macOS 10.12, is now available as a free upgrade. This new version of the Mac OS supports Java 7 and higher. This update removes Java 6, which is required by FlowJo versions 10.2 and older. We are working on a new version of FlowJo™ that will use the current version of Java.

FlowJo can now use plugins that can perform a variety of functions, including the creation of populations, creation of derived parameters, and actions when opening or saving a workspace. 

The open plugin architecture of 10.2 allows access to cutting edge tools that can be integrated into your current analysis workflows, and we will be releasing developer documentation so any tool can be integrated into FlowJo. FlowJo 10.2 includes a set of tools for discovery including downsampling, tSNE and CellOntology. You'll find these as 'plugins' in the populations band -- each offers one-click access to powerful tools to reduce any number of parameters to two and to query a database to name unknown populations. 

New Features:

•Increased the number of parameters that FlowJo can analyze to 1000

•Added a field to allow specification of R's path in prefs (Diagnostic Panel)

•Better interface for Licensing Preferences Panel in the case where a computer has many hardware addresses.

•Updated EULA to raise the awareness of the fact that you may not install FlowJo on a VM.

•Unchecked 'Display other X/Y parameters than in parent plot' as default in Gates Preferences

•Removed the option to downsample when concatenating files. (Downsample before you concatenate if desired.)

Full Release Notes

Release Notes:

• Note: Workspace file format has changed – workspaces created in 9.9.6 cannot be opened in older versions of FlowJo.  (Save as XML to read in older versions)

Features:

• Population comparison platforms allow selection of tSNE, LDA, and PCA parameters
• New platforms:
  • Bivariate Difference Gating (BDG): Compare two parameter plots, such as tSNE maps, and gate on the differences.
  • List Value Gating: FCS files concatenated by FlowJo from multiple files can be sub-gated to select groups of files from similar samples.  For example: concatenate clinical specimens, and then gate on all data from only control subjects, or only female subjects, or any other criteria).
  • Mapped BDG: A combination of List Value Gating and BDG that allows you to compare and gate on differences between groups of subjects.

• Major Speed (3x) and Memory optimizations 
• Polychromatic 'Y by Y' plot in the Layout Editor
• tSNE can now be initialized from LDA or PCA parameters
• Many other fixes and improvements
• See full v9 release notes here!

New Dimension Reduction Platforms:

PCA (principal component analysis): http://docs.flowjo.com./v9/flowjo-v9-documentation-home/platforms/pca/

LDA (linear discriminant analysis -- optimal separation of multiple subsets) http://docs.flowjo.com/v9/flowjo-v9-documentation-home/platforms/lda/

Layout Editor accepts text pastes (and will create text object or table if tabular format)

Parameters selection for tSNE, LDA, PCA, and layout editor N x N plots made more powerful.

By default, most menus will no longer show uncompensated fluorescence parameters for compensated files. (Change this behavior by global preference, or at a single time by holding down the option key when clicking on the menu.)

Compensation Wizard displays the SSM with a heat map background to highlight parameter pairs with high spillover-spreading.

Sample Get Info has a new dialog window interface, with new capabilities (like showing a table of keywords in all samples in the group; showing only interesting keywords; showing only keywords with distinct values.)

FlowJo will notify the user if a Table or Layout Batch operation points to a group that has been deleted.

FlowJo now shows 9 decade log scale for Yeti files.

Fixed reading certain XML workspace files.

Fixed crash while editing compensation matrix (from v9.9.3)

OSX 10.2 to 10.8 (will not work on OS X 10.9 and above).

512MB RAM, 2GB recommended.

USB2 port for dongle option.

Network adapter for Serial number option.

Network adapter and Internet access for site license option.Optimized for Intel and PPC Macs

Supports multiple processors, up to 8.

Improved Compensation Wizard

PolyChromatic Plot and PolyVariate plots

Molded and Spider Gates

Enhancements in Layout and Table editors

Custom formulas in the Table Editor

New Math Functions

Multiple Keyword Editing Options

OSX 10.5 or higher

512MB RAM

USB port (dongle option)

Network adapter for an off-line V8 serial number

Network adapter and an Internet connection for Site License serial number.