Navigation Bar

The navigation bar is the control center that allows you to choose what context will be displayed in the central panel.

The navigation bar (Figure 1) is the control for choosing what tool is displayed in the Discovery Panel (located in the center of the workbench), a well as in the Context panel and Context navigation bar (located respectively on the right side and far-right side of a workbench). The tools are ordered from top to bottom in the order of the expected workflow, beginning with annotation in the Metadata manager, and ending with reporting via the Report Editor.

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Figure 1. Navigation bar

Controls available are:

Metadata manager

Data annotation allows for improved organization, ordering, and iteration within FlowJo^TM. Information about the data, metadata or keywords, can be added to your Flow Cytometry Standard (FCS) files either at the time of collection using the acquisition software or post-acquisition in FlowJo^TM. All cytometers will automatically set minimal information through the use of keywords, which are short strings of text added to the header of the FCS files identified by letter codes. The list of keywords required by the FCS standard is available here. To add additional keywords either follow the instructions in your acquisition software or do it in FlowJo^TM afterwards as described in this section of the documentation.

Sample Quality Control (QC)

Sample QC is crucial in sample analysis. Despite all care during samples preparation and instrument setup, issues could arise during the acquisition step. Those issues may result in the alteration of parameters measurement and can lead to false discovery.

Compensation / Unmixing

The compensation platform allows for post-acquisition compensation using the traditional approach, spectral compensation, or either one ameliorated with AutoSpill.

Graphs and Gating

The Graph is the analysis interface that facilitates data visualization and gating in a single interface.

Platforms

FlowJo^TM has several analysis platforms that provide capabilities beyond the gating and statistics used for most simple data analysis.

Tables

Tables are used to show summary statistics, sample keywords, or parameters for either exploration or reporting of results. Tables are generated and can be visualised within FlowJo^TM, or available to export to many formats so they can be accessed in other softwares.

Charts

Charts help to visualize data from tables.  After creating a table, the charts tool can be used to create a visualization of that table in different graphs (i.e.: bar charts, pie charts, Violin Box) that tells the data story in a visual, easy to interpret way. 