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 »

FCS (Flow Cytometry Standard) is the standard that all files are created by flow cytometers follow. 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… Read more »

FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data.

The Population Comparison platform is a tool used to assess statistical differences in populations between files. Comparing distributions of data is an important goal in many applications. Many experiments are designed to test whether two populations are statistically significantly different (control vs. test sample, two control populations, etc.). Others attempt to measure a response to stimulation… Read more »

The kinetics platform is used to create models of changes in an individual sample across the collection time. The kinetics platform uses the collected time parameter to create a graph of time versus the statistic of interest for the sample.  The user may then divide the data into as many time ranges as they choose, or may select Auto-Range… Read more »

FlowJo’s Proliferation platform allows users to quantify many different common types of proliferation assays which look at cell division over time. FlowJo’s Proliferation tool looks for a pattern typically expressed by cells loaded with fluorescent dye and allowed to divide. Typically this tool is used to model the sample as it undergoes 3-6 divisions and generate… Read more »

The Workspace Window in Depth: *For a more general overview of the workspace, go here. Figure 1. The workspace window. The Workspace window is organized in three main sections (shown in image above): 1) Tasks and Bands: 2) Groups: 3) Samples and sample analysis: The Workspace uses a variety of additional indicators to help with analysis:… Read more »

A keyword can be entered into one sample and quickly applied to the rest of the samples in a group. To copy a keyword value to an entire group, use the ‘Copy value to group’ button located in the Keywords band in the workspace ribbon by default. this band is shown in Figure 1. Figure… Read more »

FlowJo provides a quick and easy way to add important Statistics to your analyses and reports. Statistics are treated like other nodes in the Workspace. They can be added singly or en-masse to sub-populations, layouts and tables (via drag-and-drop or thru the Add Statistic dialog). A full list of statistics available for use can be found here,… Read more »

This page details the statistics that can be selected from the Statistics Dialog window. Scale space vs. graph space Intensity is in arbitrary units and can be expressed as scale or bin numbers. The scale values take into account scaling factors such as the gain setting for the parameter, and are the values displayed on… Read more »