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FlowJo Portal license: Updating to the latest version of FlowJo for FlowJo Portal license holders is easy! Simply download the latest version of FlowJo v10 above and sign in with your FlowJo Portal ID.
If you would like more information about your dongle, please call 1-541-201-0022 or email license support with the dongle serial ID of your USB dongle. Instructions for locating your dongle serial ID can be found here under Locating your Dongle ID.
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.
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.
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.)
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.)
The environment is presented as the Workspace, which contains a list of loaded samples (experimental data), statistics, gates, and other analyses, as well as tabular and graphical layouts. The workspace is saved as a FlowJo document on your hard disk; when you reopen the document, you will see your analysis as it was when it was last saved.
Our web manual is a search-able set of pages which explains the many features and functions in FlowJo. Please use the navigation bar at left to explore, and note that pressing the question mark button in any window in the FlowJo application will launch a web browser and access a help page relevant to that window.
As a note, we are pleased to be able to frequently update FlowJo to provide new features and analysis capabilities. Therefore, we always recommend that you download the most recent version of FlowJo from: www.flowjo.com/solutions/flowjo/downloads
Listed below are the changes made to FlowJo since the release of FlowJo, version 6.4, on November 16th 2005. The changes are listed in reverse chronological order. Within each revision are listed the new features (major and minor), and any bug fixes.
Fix: Disallow compensation matrices with same name (will rename them "-1", "-2" etc)
Fix: Properly scale FCS 3.0 floating point parameters with a $PnR that is not a power of 2
Fix: Trying to load a data file for which you don'thave read privileges now shows error message.
Fix: FlowJo can now handle the situation where the user sets custom transform visible decades to zero (bad value.)
Note: Workspaces saved by 8.5 will not be read by 8.4. However, you can save a workspace as XML and open it in 8.4 (you will lose information regarding new 8.5 features, but everything else should be fine).
Workspaces saved in FlowJo v6.1 cannotbe directly opened with earlier versions of FlowJo. However, you can save a workspace as XML (File->Save AsXML...); that file can then be opened in FlowJo v6.0. Please see notes on XML under "Workspace" below.
SciBook . The SciBook is a place where you can store pictures, text, tables, or custom annotations. The SciBook is stored with the workspace; you can use it as a permanent record of your analyses, as a temporary holding place for outputs, or just tokeep notes for yourself. You can paste graphics, text, or tables from anywhere in FlowJo into the SciBook (the Graph window, Platforms windows, Layout Editor, Batch Layout View, and Table View all have buttons that will directly copy theircontents into the SciBook). Contents in the SciBook do not change-therefore, if you change a gate, delete a sample, or make other modifications, the SciBook contents will not be modified. Once in the SciBook, you can copy into other programs,print, or simply just view. The SciBook gives you an interface to add comments about each item that you insert, and records the date and time that the item was inserted.
The SciBook is meant to evolve; we look forward to your comments regarding which features you use the most, what features you would like to see in the future, and what you do (and don't) like about it!
Boolean gates . You can now create a gate which is a Boolean combination of any existing gates (i.e., "and", "or", and "not" combinations). Boolean gates are "live", meaning that they will reflect any changes to the gates on which they depend. FlowJo canalso automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates. For example, if you have a sample which was stained on different parameters for IL2, TNF, and IFNg, you can create a positivegate for each of the three cytokines (for example, a histogram gate). Then use FlowJo's Boolean Combination to create the 8 gates that represent all combinations of expression of the cytokines (e.g., IL2+TNF+IFNg+, IL2+TNF-IFNg-, etc.). Tocreate or edit Boolean gates, choose the parent subset(s) and select the menu item "Boolean gates..." under the "Platforms" menu.
Derivedparameters . You may now create a derived (computed) parameter that is any algebraic combination of existing parameters. FlowJo allows you to specify arbitrarily complex formulas, and includes a wide variety of mathematical functions that you can useto transform the data. This platform can be used in FRET calculations to create a parameter that reflects the efficiency of resonance energy transfer.
Layout Editor: NewStatistics Table. FlowJo now renders tables of statistics in a beautiful and highly customizable way in the Layout Editor. You can copy tables (either by dragging them from the Table Template Editor to use with Batch iteration, or directly from a completedtable). Or, you can create them from scratch, adding your own statistics and keywords and other information. Statistics Tables in the Layout Editor come in two flavors: (1) Each row is from a single sample: this is like the output of the tableeditor, where statistics for subsets or the whole sample are all represented on the same row; (2) Each row can have subsets from the same sample: this allows you to view a number of statistics (e.g., MFI) on many subsets from a single samplein column format. Note that you can copy Layout Statistics Tables directly to spreadsheets (as tabular data) or to graphics programs (as their graphical representation).
Layout Editor:Overlay legends . The legends for overlays in the Layout Editor can now be customized to show statistics, keywords, or other pertinent information from each subset that is overlayed in the graphic. Simply double click on the legend to specify what should beshown.
Templates: Improvedfunctionality. This "Iterate by nth" Layout Editor feature also means that Template Workspaces that contain batched layouts will work well. A batched layout is now automatically defined to have the appropriate iterator (and discriminator) values; when youbatch a layout over every sample and save it as a new layout, the new layout is automatically defined to iterate by "nth", where "n" is the number of tubes in the original batch.
In addition, sample identification is significantly improved in FlowJo. This means that Template workspaces will fill out layout graphs as expected-FlowJo tries very hard to overcome any ambiguities that might arise because of multiple samplesfitting the criterion for a single graphic.
As the drafting of this KB the vendor is not recommending JRE 1.7.x
Make sure the only version of installed Java on your workstation is JRE 1.6.x the latest version (currently 6.43)
Per Flow Jo do the following:
On Windows7, in the flowjo install folder there is a java lax settings file that can be edited to use updated jre versions. Locate the .lax file, open with note pad and look for LAX.NL.CURRENT.VM section, comment out the current path and change to "lax.nl.current.vm=c:\\Program Files\\Java\\jre6\\bin\\java.exe" SEE Example as follows:
FlowJo will soon release an updated version of FlowJo (v11). Unlike previous upgrades, FlowJo 11 will no longer be backwards compatible with the dongle system. The UTMB Flow Cytometry Core now has a FlowJo Portal site license. This site license will offer you the ability to always have the latest version of FlowJo.
Some things you can look forward to in FlowJo v11: FlowJo Version 11 will have multiple upgraded features. FlowJo 11 will be faster, and it will be easier to compare multiple samples at one time. Additionally, there will be a new quality control feature which ensure users are looking at high quality data. There will also be increased capacity for statistical analysis including new statistical graphing features. Finally, there will be more built-in plugins for data dimension reduction (ie tSNE & UMAP) as well as clustering algorithms (ie XShift, FlowSOM, FlowMeans and Phenograph) making it easier to explore and analyze high-dimensional data.