Change your settings for the Panel Wizard, Compensation, and other special analysis platforms. Compensation: Set default compensation control group inclusion criteria. Cytometry Platforms: Set the default conditions for the cell cycle platform. Plates: Set default plate annotation selections and visualization types.

Output preferences allow you to change the default setting for graph visualizations, output from table and layout editors, and export/saving. Graphs: Set default graph type and display options in the graph window. Tables: Set behavior of new tables, formatting and include standard header and footer elements in printing. Layouts: Choose iteration/batch operation and image type… Read more »

Workspace preferences allow you to change the display and other options for the central hub of analysis in FlowJo.   Workspace: Define sample name and general workspace appearance. Fonts: Define text/font settings for Workspace,Graphs and Layouts. Gates: Set gate appearance, define frequently used gate names and child population graph types. Locale: Language, numbers and time… Read more »

The Plate Editor can annotate FCS files from plate-based assays. High-throughput plate-based assays are increasingly common in flow cytometry. Working with collections of 96, 384, or 1536 wells at a time adds additional dimensionality to the biological questions that can be asked. However, the amount of data produced presents management and annotation challenges.  FlowJo’s structured approach… Read more »

The Layout Editor has a number of options to display your graphs (charts) and annotate your data. Changing visualization and annotation: The central place to go to edit charts and add annotation is the Graph Definition Window, which can be accessed by double-clicking on a graph. Visualization options: Here are a handful of visualization options that can… Read more »

Presenting your Data for Publication or Presentation Now that you have done your analysis, you need to get your data out of FlowJo for presentation or publication purposes. FlowJo’s layout editor has all the tools necessary to make this happen. For more on actually creating the layout, start here. Follow each of the links below… Read more »

The Layout Editor is a data aware graphical editor. This is obvious for graphs, whose appearance change with updates in your gating.  It similarly applies to other items that can be created in the Layout Editor, such as statistics, equations, plates, and tables. Editing Statistics in the Layout: To display a statistic in a layout, drag and… Read more »

Tools in the Layout Editor get you from data to finished report quicker than ever before. Formatting Tools: Objects like graphs, statistics, and shapes can now be grouped, aligned, and locked. Aligning Layout Objects Lock Tool in the Layout Editor Editing Multiple Objects at Once Drawing Tools: There are a plethora of drawing tools that allow… Read more »

FlowJo offers several options for visualizing your data in the Graph Window. Once you have a graph window open, you can easily switch between graph types either by selecting the type (and/or options) from the graph menu, or by opening the options disclosure triangle at the bottom of the graph window.   Which will allow… Read more »

FlowJo v10 has expanded gating tool options to help you effectively gate your data. Isolate, divide, or group your populations for excellent annotation and analysis. Advanced Gating Tools There are several advanced tools to set Gates within the Graph Window, three of which are shown below. Autogating Tool: Sets a gate based on probability contours, similar to the… Read more »