Life Technologies Attune flow cytometers produces FCS 3.0 compliant files. Attune data files have a maximum range of about 1 million channels for both linear and log parameters, so linear parameters are displayed on a scale that extends to 1M, and log transformed parameters display on a 6-decade scale. The preferences in FlowJo (v10+) are… Read more »

BD Accuri cytometers use the C-Flow software, which produces FCS 3.1 compliant files. These data files have a range of 16.7M, so the scale appears in 7 decades when log transformed. Preferences in FlowJo (v10+) are set by default to scale the data correctly according to the acquisition display and the format of the file.  You can… Read more »

FlowJo now supports the import of CLR (CLassification Results) and CSV (Comma Separated Values) files.  This document describes the various file formats, the results of importing them for a sample population, and how to use them in FlowJo. These features are still early in their adoption and development. Potential Use Case(s) 1. Doing a probabilistic study… Read more »

Need to find that complicated sub-population? FlowJo’s Boolean gating options make it easy to find cells that express a and b, x or y but not z. FlowJo’s hierarchical gating method automatically designates basic AND Boolean logic by showing one sub-population indented and underneath another in the Workspace window. You may wish to do more complicated… Read more »

FlowJo v10 let’s you see the “big picture” by presenting all possible Boolean Combination gates of a population. In FlowJo v10 you can create simple Boolean gates, or for more complex analysis, you can use the Boolean Combination Gates option to generate Boolean gates of any existing population using all the Boolean functions. For example,… Read more »

Badges succinctly provide a wealth of information in the workspace. The FlowJo workspace adorns samples with new icons, presented in three columns – known as badges. The badges will inform you of whether your samples have been compensated or not, if there were any serious anomalies during acquisition, and which samples have been or are… Read more »

There are many times when it is useful to include additional information in an analysis, e.g. annotation recorded during experimental design in a spreadsheet. FlowJo makes it easy to address this and add additional keyword-value pairs to the Workspace. There are a variety of keywords that exist in FCS files by default. For information on those keywords,… Read more »

FlowJo software is complex, and analysis can often be accelerated by adopting the use of keyboard shortcuts. Many actions in FlowJo have been assigned shortcuts. Through using modifier keys like shift/ctrl, alt (option on macs), and cmd (for macs), as well as the right-click menu, you can often find shortcuts to context-specific functionality to aid… Read more »

Frequently Asked Questions for most Technical Issues. For General FAQ, including dongle/license assistance, please view this document. 1) How do I generate publication quality graphics? 2) How do I place statistics in the table editor? 3) How do I place graphs in the layout editor? 4) How do I add statistics to my samples/populations? 5)… Read more »

Many of the operations you will perform in FlowJo  are executed by dragging and dropping. For instance, to copy an analysis gate to another sample:  click on the sub-population gate, and while holding the mouse button down, drag until the desired destination sample (or sub-population) is highlighted; then let go of the mouse button. FlowJo… Read more »