Manual gates are used to set gates by intensity or percentile. To manually enter a gate from the Graph Window, select the desired parameters using the X and Y axes drop-down selectors, and then choose Manually Enter Gate from the “Graph” menu at the top of your screen (this can also be accessed with command + G… Read more »

Magnetic gates allow you to accurately gate on populations that may shift slightly between samples. During your analysis, you may be interested in gating on the maximum number of events of a particular population for several different samples. However, these populations may shift slightly from one sample to the next. For example, the forward scatter and side… Read more »

FlowJo has several tools for Drawing Gates within, around, or outside a population of interest. FlowJo’s drawing tools will help you isolate that tough rare population and prepare your workspace for downstream analysis. FlowJo has 3 main types of gate drawing tools; shape fitting, quadrant, and line (see figures below). The types of drawing tools available depend… Read more »

Spectral spreading affecting your data? FlowJo v10 has the cure. Curly quad gates are designed to account for the error introduced by intensely fluorescent data. Why should we use curly quadrant gates? The curly quadrant tool is a gating tool that creates a quadrant gate with curved arms. It is useful for data that exhibits spread… Read more »

One of the biggest advantages of FlowJo is the ability to copy analyses (gates, statistics, kinetics, cell cycles, etc.) from one sample to another by drag and drop. In general, this is accomplished by clicking on the analysis (a gate, statistic, or population node), and dragging it to the destination. The node is added on… Read more »

Need to tighten that gate to remove doublets or debris? Was that lymphocyte gate too generous? FlowJo allows you to adjust gates at any point during your analysis with immediate updates to statistics, tables and layouts. Analyzing flow cytometry data often requires adjustment to previously defined gates in order to accomodate or remove certain groups… Read more »

Quickly export a Graph Window in a variety of formats to generate a figure in a report, email an image of results to a colleague, or update a webpage. Whatever your need, FlowJo allows you to save and move graphs to multiple programs. All Graph Window plots can be exported as image files, but histograms and… Read more »

FlowJo makes it easy to view one population on different parameter sets.   For instance, you may be looking at multiple expression profiles of cytokines at once. Therefore, it would be helpful to see the sample population being displayed as a histogram plot for IFN-g, TNF-a and IL-2. To duplicate a graph window, click on the Duplicate… Read more »

In a dot plot display, FlowJo draws dots for events. The default number of dots to draw is 8000. You may change the number of events drawn in a dot plot by clicking on the Options disclosure triangle in the graph window (below). To reset the dot plot to the original 8000 dots, just type in… Read more »

FlowJo v10’s graph window now includes a navigation breadcrumb bar: This can be used to quickly jump to a different level in the hierarchy, or to jump to a sibling gate along the hierarchy. In the example above, the leftmost “>” symbol is a pulldown menu that will navigate between different ungated samples. Clicking it… Read more »