FlowJo can save your analysis in 4 different ways, which are detailed below: Workspace (WSP) Template (WSPT) Archive (ACS) Excel (XLS) 1. Workspace (WSP) The workspace is the central hub for all activity in FlowJo, and saving as a workspace will save: A list of all the samples added to the Workspace A list of all… Read more »

What keywords are associated with my FCS files? What does my compensation matrix look like? FlowJo v10 lets you quickly assess this information and more with the Inspect tool. You can access Sample Properties/Information by selecting a sample in the Workspace and choosing Inspect from the Populations band of the Workspace task in the Workspace, command-clicking/ right-clicking… Read more »

If sample files are moved to a new location, or a folder in the file path is renamed, a FlowJo workspace may not be able to locate the sample files when re-opened. If this occurs, don’t worry. There is an easy way to reconnect files to the workspace without reanalyzing the data. How to reconnect sample files to the FlowJo Workspace: The… Read more »

The Workspace is your starting point in FlowJo. Figure 1. The FlowJo Workspace. The workspace stores sample reference lists, sample analysis, supports the movement of analysis from sample-to-sample, sample-to-group or workspace-to-workspace and serves as a launch pad to other areas of the program such as the Graph Window  , Table  and Layout editors  and all specialized analysis platforms…. Read more »

The experiment annotation platform assists with describing your data and experiment according to the MIFlowCyt standard. The “Annotate Experiment” tool, which can be found in the the Experiment band, provides a dialog to enter the experimental description. Figure 1. The Annotate Experiment tool. This dialog is designed to comply with the proposed Minimum Information about a… Read more »

Creating a keyword value series allows you to add a column of meta data to your workspace with a pattern to it. Instead of manually typing in a series of values into the workspace, the keyword value series tool allows you to describe the pattern the annotation will have and quickly implement it.  One of FlowJo’s most powerful features is… Read more »

FlowJo version 10 has a new preference setting that allows users to customize the data scaling based on the cytometer used to collect each file. (*Please note – Instrumentation companies are constantly releasing updates to their software and do not always notify us of changes they have made to scaling keywords. If you cannot get… Read more »

Run FlowJo in your preferred language FlowJo v10 is the first version capable of running in multiple languages, and international number and date settings. When FlowJo is launched for the first time, it will attempt to detect the computer’s localization, including numerical formatting. In the United States, a thousand will be rendered as “1,000.00” whereas… Read more »

Stop shuffling around looking for files. Simply drag and drop what you got into the Workspace and begin your analyses! FlowJo’s intuitive interface, a hallmark of good design, makes it easy to start analyzing your data. Samples can be added to the Workspace in several ways. Drag and Drop: any file or folder of files can… Read more »

Groups in FlowJo are surrogates for a set of FCS files, and are thus the basic functional unit of anyone working in an effective high-throughput manner. Any action that you would like to apply to more than one file can be achieved by applying that action to a FlowJo Group. FlowJo uses Groups in the… Read more »