Plate Editor

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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 »

Graph Options and Annotation

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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 »

Export, Output, and Printing

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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 »

Statistics, Tables and Equations

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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 »

Graphic and Drawing Tools

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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 »

Data Visualization and Display

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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 »

Advanced Gates and Gating Tools

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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 »

Keywords and Annotation

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Data annotation allows for improved organization, ordering, and iteration within FlowJo. Meta-data, information about the data, can be added to your FCS (Flow Cytometric Standard) files either at the time of collection using the acquisition software or post-acquisition in FlowJo. All cytometers will automatically set minimal information through the use of keywords, which are short… Read more »

FlowJo and Your Cytometer

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As you probably know, FCS (Flow Cytometry Standard) files are created by flow cytometers. FlowJo can read and analyze FCS files from any cytometer. Each cytometer will scale your data slightly different during acquisition. The FCS3.0 standard provides for up to 32 bits of data, or a range in the scale of 2^32. Instrument scaling range… Read more »

Advanced Features

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FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data. Archival Cytometry Standard (ACS) are container files that compress workspaces, FCS data files, and plugin outputs into a single compressed .zip file, helpful for archiving, sharing, or working with remote data storage. Templates are an excellent way to… Read more »