FlowJo is like the Swiss army knife of Flow Cytometric analysis programs. It contains tools for all of the jobs you need to easily and efficiently perform any type of data analysis from start to finish.

New Version 6 Features

Dashboard. 

Version 6 includes a Dashboard Widget especially for FlowJo.  Dashboard is the Tiger Operating System's new short cut access to Java applications.  With the help of a provided plug-in, you will use Dashboard to quickly investigate fluorescence curves of several common fluorochromes. After installing the plug-in, you'll be able to add fluorescent calculators to Desktop Dashboard.

Spotlight. 

You will now find a 'Spotlight Importer for FCS Files' in FlowJo Version 6.  Spotlight is the Tiger Operating System's new fully integrated, fast, and efficient search tool. With the help of the accompanying plug-in, you will use Spotlight to search on FCS keywords stored in CellQuest (and other) files. Spotlight is as fast and efficient as the search tools you use to find what you want on the web. After executing the 2-step installation procedure, you'll be ready to run your first search in Spotlight. Just click on the magnifying glass icon on the top right corner of desktop!

Autogate tool. Point. click. gate. It shouldn't be any harder. And, with FlowJo's new Autogating tool, it can't get easier! FlowJo's autogating tool has an almost prescient knowledge of where you want the gate-an effect made possible by the instantaneous feedback of where the gate will be as you mouse over the graph! Choose the new autogating tool in the graph window, or simply hold down ctrl-option as you move the mouse over any bivariate graphic. (Note: if you hold down the mouse button as you click to create the gate, you can then track the mouse to inflate or deflate the gate to size it with even more precision!)

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 to keep 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 their contents 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!

Backgating Analysis. Validating gate positions is one of the most important aspects of multiparameter Flow Cytometry. FlowJo now provides you with a tool to view the effect of every gate on your final gated population! In any graph window for a subset that is gated more than once, you can choose "Backgating Analysis." under the Graph menu (or, click on the Backgating button that appears near the top right of the window). FlowJo shows you a window where each level in the gating hierarchy is displayed, with the final gated population overlaid at each level. This overlay is a backgating overlay: in other words, it shows what the final gated population would look like without that level's gate! Therefore, you can quickly scan to see if any one of your gates is positioned incorrectly. The backgating display can be printed, copied, or saved in the SciBook (see below). Note that the Layout Editor can also show a version of the backgating analysis, by choosing "Show Ancestry" and selecting the "Backgating" option for a graph

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 can also 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 positive gate 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.). To create or edit Boolean gates, choose the parent subset(s) and select the menu item "Boolean gates..." under the "Platforms" menu.

Derived parameters. 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 use to 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: New Statistics 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 completed table). 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 table editor, 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 sample in 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 be shown.

Layout Editor: Iterate by "nth" sample. Sometimes you just want to do batch iteration where the order in which you collected the samples defines how you want the output to appear-for example, every three tubes comes from a single sample, where the first of the three is a control, and the other two are two different panels. FlowJo lets you easily specify such a design by using the "Iterate by nth" option. (Choose "Iteration options" under the layout menu). In this example, you would iterate by "every 3rd sample", telling FlowJo to group tubes into samples of 3. This significantly simplifies batch operations. All new Layouts are created with the "Iteration by nth" (n = 1, i.e., every sample) by default.

Templates: Improved functionality. 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 you batch 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 samples fitting the criterion for a single graphic.