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.

If you are a FlowJo user we recommend that you hang tight until we release FlowJo 10.3.

Version:
Minimum
Requirements:
Recommended
Requirements:
Features:
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• 2GB RAM
• Core II Duo processor or better
• OSX 10.6.8
• Apple Java Runtime Environment 6. Available at the following link, not viewable through Safari browsers:
Java for OS X 2015-001
• USB port (dongle option)
• Network adapter for an off-line serial number
• Network adapter and an Internet connection for Site License serial number
• 16GB RAM
• Intel i7 quad core processor
10.2:

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



*Attention users with offline serial numbers: Since version 9.9.3, FlowJo requires a new version serial number for offline use. If you receive a serial number error message, please contact us so that we can renew the serial number for you: office@flowjo.com or call us at [+1] 541-201-0022
OSX 10.4
Compatible with Mavericks
Native support for G3,4,5 and all Intel based systems.
2GB RAM
OSX 10.5 or higher
8GB RAM or higher
Version 9.9.4:
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)

Version 9.9.3
•Spectral Compensation - compensation via unmixing the spectrum of each fluorescent probe, a new visualization for fluorescence spectrum, and an optimized calculation option.
Documentation site for new 9.9 features:
Spectral Compensation
tSNE
Downsample Gate
•Parameter menus will now hide all uncompensated fluorescence parameters, not just those with compensated equivalents (if preference set)
•Bug fixed that caused occasional incorrect time parameter scaling on certain FCS files
•Bug fixed regarding custom transformation calculations on spectral compensation matrices.

NOTE: New workspace file format; older versions will not open.

Version 9.9:
New Features:
Fixes the first double click in Layout editor for the "Create NxN plot" dialog
Fixes a connectivity issue with addressing a new FLS site for verification
New Downsample gate type with options for deterministic (always return exactly the same subset of events) and random (will generate a different subsets of event each time the node is recomputed) downsampling of events from a selected population.
'live' tSNE platform for data reduction and discovery visualization which creates tSNE parameters; can create movies of tSNE process with population overlays.
Please Note: Workspaces created in this version will not be compatible with older versions i.e. they are not backward-compatible.

Version 9.8.5:
Bug Fixes:
Fixed crash when Closing a workspace while loading samples.
Fixes a rare picket fencing display issue.
Workspace optimization deleting large number of samples.
Version 9.8.3:
• Intrachannel randomization to avoid picket-fencing is now down deterministically so gates always include the same events
• Minor fixes to workspace XML format

Version 9.8.2: Minor bugs fixed

v9.8.1
Bugs Fixed:
• Enable General Undo no longer crashes when enabled.
• Graph Definition font sizes for gates and labels now set the fonts for the correct elements.

v9.8
Major new features:
• Workspace files are highly compressed--as much as 90% smaller
• Memory allocation compressed and multiprocessing optimized - particularly for new Mac Pro's

Minor new features:
• Table Editor puts bullets in cells when the sample or gate is missing
• Rescale Gallio data using CXP preferences
• Better data file exporting (e.g., include keyword/values from FCS header)
• Grouping of graphics objects is preserved in PDF output

Bug fixes:
• Concatenate does not crash if samples are missing needed parameters
• Properly handle out-of-range ("illegal") floating point FCS3.0 values in some vendors' files
• Properly save Workspace column preferences
• Concatenate properly sets time parameter values even if files are out of order
• Various minor bug fixes

Changes since 9.7.2 include:
Parameter menu in multi-item layout info dialog are now sorted per preferences
Kinetics time slices have the proper durations for subsets previously gated on Time or Event #
Minor performance enhancements and bug fixes

Performance enhancements included as of 9.7.2:
New preference to automatically add a QC parameter to each file that shows how consistent data collection is across time. This parameter can be gated on to remove "bad" data segments caused by clogs or other instrument issues leading to temporary disturbances in fluorescence measurements.
Fix a bug causing a crash when reading some XML workspaces Tweak memory management to improve performance for workspaces with thousands of files
Allow as many dots as desired in vector graph plots
Concatenate files: if files have different comp matrices, then only export fully compensated parameters
Concatenate files: properly concatenate even if files have parameter lists in different orders
Fix percentile calculations in table summaries (interpolate between data points for an intermediate percentile)
Fix: occasional crash from copy in layout editor into PDF format
Fix: Abbreviated axis notation (1.5M was shown as 1M)
OSX 10.4
Compatible with Mavericks
Native support for G3,4,5 and all Intel based systems.
2GB RAM
OSX 10.5 or higher
8GB RAM or higher
Changes since 9.7.6:
Identical to v9.7.6 with the addition of accepting BOTH v9.7 and v9.8 serial numbers.

Changes since 9.7.2 include:

Parameter menu in multi-item layout info dialog are now sorted per preferences
Kinetics time slices have the proper durations for subsets previously gated on Time or Event #
Minor performance enhancements and bug fixes

Performance enhancements included as of 9.7.2:

New preference to automatically add a QC parameter to each file that shows how consistent data collection is across time. This parameter can be gated on to remove "bad" data segments caused by clogs or other instrument issues leading to temporary disturbances in fluorescence measurements.
Fix a bug causing a crash when reading some XML workspaces Tweak memory management to improve performance for workspaces with thousands of files
Allow as many dots as desired in vector graph plots
Concatenate files: if files have different comp matrices, then only export fully compensated parameters
Concatenate files: properly concatenate even if files have parameter lists in different orders
Fix percentile calculations in table summaries (interpolate between data points for an intermediate percentile)
Fix: occasional crash from copy in layout editor into PDF format
Fix: Abbreviated axis notation (1.5M was shown as 1M)

To download legacy versions of FlowJo, click Here