The outline of the Reference Manual is shown below. Click on any topic to learn more about it; or use the navigation buttons on the left to go to the overview of any section.
- Workspaces: an overview
- Reading samples into workspaces
- Batch analysis
- Dragging and dropping (copying) analysis nodes & trees
- Keyword Search and Replace
- Graphic displays
- Gating: Creating new subpopulations
- Polyvariate Plot shows more than 2 parameters on a 2D graph. This allows the user to define complex populations of cells using one gate.
- Vertex Gates - link gates' vertex coordinates to a summary stat of another gate.
- Overlaying graphs.
- Creating derived parameters (time, ratios, log <-> linear conversion)
- Compensation Wizard Create compensation matrices quickly and rigorously.
- AutoCompensation Scripting Find compensation samples, gate them, create the compensation matrix, and apply the matrix to experimental tubes.
- Calibrated Parameters Quantitation of absolute molecules per cell.
- Cell Cycle
- Proliferation Studies
- Population Comparison
- Multiple Sample Comparison
- Overlay Graphs
- Computing Background Gates
- BiExponential Transformation Visualize compensated data without cells squished against the axis and digital data without picket fences.
- Layout Editor - Can be dragged (or copied)from one workspace to another.
- Copying graphs to other programs (generating publication-quality graphics)
- Tables - New user interface with batching and formulas.
- Exporting raw (gated) data for analysis by other programs
If this is your first time learning about FlowJo, you should read the pages describing the general concepts behind FlowJo. You may want to run through the tutorials, which will introduce you the program by analyzing a real experiment. To see how the current version is different from older versions of the program, click here.
As you use the application, you will see that FlowJo is littered with Help buttons. Almost every FlowJo window has a help button and virtually every time FlowJo notifies you of a problem or asks you to make a decision, there will be a help button. When you click on these help buttons, FlowJo will launch a web browser (such as Netscape) and bring up a page that gives you specific information about that particular window, error message, or the decision options. You can also press the "help" key on your keyboard at any time and get information about the front-most window. Use this help feature frequently! You will find many hints about using FlowJo more efficiently. You might also want to check on the Frequently Asked Questions to get some hints once you are familiar with the program.
This online help can be downloaded in its entirety to your computer for faster access. Click here for more information.
Both the application and the help pages are dynamic: they are being continuously developed and improved. Therefore, we want to hear any and all suggestions about how to improve them! Please report any problems, suggestions, or questions for which you can't get answers; the easiest way to do this is by E-mail. [More information about making a report]