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 4 Features

4.4 - New Printing Model (full list of new features in 4.4)

Printing layouts and layout outputs has been completely revised. One of the best ways to see how this functionality can be used is to create a “Tiled View” batch report, and choose to Print this view—the new interface will show you the various options you have. These options are also available when you choose to directly print a batch output.

Importantly, you no longer need to (or can) do “Page Setups…”. Rather, FlowJo will automatically adjust printouts to whatever printer you select when you print. By default, FlowJo will also automatically position your graphics to fit best on each page (i.e., Portrait vs. Landscape, centered, and sized as large as possible). There is a new interface that lets you exert complete control over how you want the outputs to look—including the number of panels per page, the orientation, whether or not to suppress headers and footers, etc. The “Page Setup…” command from the Layout Editor now lets you select only whether you wish Portrait or Landscape mode, and whether you want headers and footers printed. Note that when you click to resize the page boundaries in the view, FlowJo will switch between Portrait and Landscape mode automatically as needed. Printing is now a breeze!

In addition, printing of Workspaces and Tables is also completely revised. These are always scaled to print no more than one page wide (although they can be several pages long). FlowJo chooses the best layout to print this tabular data; no “Page Setup” is needed. Finally, printing of analysis platforms and graph windows is significantly improved along the same lines.

All printed pages can be customized through the Preferences selections. You can define a variety of header and footer information (for example, the user, computer, date, time, workspace, layout name, group name, etc.) as well as a graphic that is to be displayed within each header, footer, and/or body of every printed page!

4.3 - Display Transformation
FlowJo version 4.3 has implemented a new way to visualize compensated data so that cells are not squished against the axes. This transformation also removes picket fences from digital data. The data is not altered in any way - FlowJo's transformation displays the data with alterations to the log axes so that the scale has a zero and a negative region. This allows you to view populations that formerly had cells squished against the axis as nice symmetrical clusters. For more information, please visit our Display Transformation web pages.

4.0 - FlowJo has carbonized to fully take advantage of OSX. In addition, we have added several exciting new features to Version 4. The Cluster platform (using the algorithm developed by Dr. Mario Roederer) is an exciting tool for exploring your data. This algorithm automatically finds subsets based on staining patterns or cells in a sample. The Multigraph Overlay platform displays many graphs of a single sample - allowing you to view every parameter of your sample. Each subpopulation is displayed as a different color so that forward and back gating is easy.

Keep your data and analyses organized!

Keeping track of your analyses is easy with the FlowJo Workspace window. FlowJo organizes all of your data, gates, analyses, statistics, tables, and reports in a Workspace window. [details]

Gating FlowJo allows users a great deal of freedom with defining subpopulations, regardless of the number of parameters. The hierarchical display of gated subpopulations shows the gating tree simply and clearly. [details]

Drag and Drop is used to propagating any analysis (gates, statistics, platforms): to other samples, or to entire experiments! [details]

Save time with batch processing!

FlowJo is a program that doesn't just analyze individual data samples. Rather, the focus is on analyzing groups of samples, experiments, or even multiple experiments at once. The real power of FlowJo as an analysis tool becomes immediately evident when you start to do Batch operations (repetitive analyses performed on multiple samples). [details]

Within a workspace, you can Group samples by various attributes–a group is a collection of any or all samples with a similar attribute (tissue, sample source, panel, collection date, etc.).  Groups are really the powerful feature of FlowJo: when you perform an operation on a group, it performs the operation on every sample belonging to that group. Thus, you can apply a gate or a statistic to a group, and that gate or analysis will be automatically performed on all samples! [details]

Data Export and Publication Quality Graphics

FlowJo is loaded with many options to represent FACS data graphically [details] and was designed with publication quality graphics in mind. [details]

Compiling your data into tables of statistics and graphical reports is easy with FlowJo. You can design graphical and tabular layouts as simple or as complex as you wish, with complete control over the fonts, colors, and styles of the graphs. With a single click, you can copy the outputs to your favorite spreadsheet or graphics package--where you can ungroup all of the elements for individual editing. [details]

Analyze any type of data!

Compensation
Sometimes your data is not properly compensated... sometimes, it is not possible to compensate your data on the machine because of the complexity of the analysis. FlowJo's compensation platform makes compensating data much easier than compensation on the machine; you are always guaranteed a correctly-compensated output! [details]

Cell Cycle
FlowJo gives you a sophisticated, yet easy-to-use interface to model DNA/Cell cycle data. You can simultaneously compute several different standard models, with the ability to constrain different model parameters with the click of a mouse. [details]

Kinetics
FlowJo provides a sophisticated platform designed to analyze and display time-dependent data. From this platform, you can compute the maximal response time, the slope of a response, the fraction of responding cells, etc. [details]

Proliferation
FlowJo models proliferation data obtained using cell tracking dyes such as CFSE. FlowJo presents a graphical display as well as information about each generation in the subset. The proliferation platform also provides information about the fraction of cells from the original population that have divided, and the number of times these cells have divided. In addition the FlowJo Proliferation Platform draws gates that separate each generation. [details]

Calibration
FlowJo's Calibration Platform gives you the ability to convert your fluorescence measurements into a calibrated unit, such as absolute number of molecules per cell. All you need is a calibration standard, such as a bead set with defined fluorescence values. FlowJo automatically finds the bead peaks; once you enter the corresponding value for each peak, FlowJo will determine the correct calibration function. [details]

Derived Parameters
FlowJo lets you define new parameters for samples. These include the ability to add Time as a parameter (for performing kinetics analyses), to compute the ratio of two collected parameters, or to convert between log and linear scaling. Derived parameter definitions can be copied to entire groups of samples. Let FlowJo calculate a ratio of two parameters, add a time parameter (in case you want to do Kinetics analyses), or convert between log and linear scaling.

Population Comparison
The Population Comparison Platforms allow the direct comparison between different samples or subsets. FlowJo can take two or more samples and analyze them to determine how different the distributions are. Comparisons can be univariate or multivariate, and you can rank multiple samples by their similarity to controls. These platforms take advantage of the exciting new comparison algorithm - Probability Binning. This algorithm even allows the creation of a gate to display the difference between two populations. [details]