Compensation has undergone a major redesign for FlowJo Version 10! Compensation in flow cytometry is the process of correcting for fluorescence spillover emissions. The detectors, or channels, in the instrument are designed to detect a very specific range of emissions. However, the fluorophores used in flow cytometry do not adhere to the exact range of emission… Read more »

Whether compensation comes from your data as Acquisition-Defined, or is generated via FlowJo’s compensation wizard, the resulting matrix of values will be stored in XML in the FlowJo workspace document. To save a matrix to its own stand-alone file, use the Matrix Editor. The matrix editor is easily accessed by double-clicking a sample’s compensation badge… Read more »

Probably the first thing you’ll notice about the Workspace window changes is the new special Group “Compensation” :   FlowJo scans your files as you load them into the workspace, and if any of them match our criteria for compensation controls, they will be added to this group. You can see the default inclusion criteria for… Read more »

Can my compensation control be too bright? No.  In fact, the brighter, the better!  Compensation controls allow the software to calculate how much spillover fluorescence occurs from that level of primary fluorescence.  The equation calculates the ratio of the DIFFERENCE in the secondary fluorescence over the DIFFERENCE in primary fluorescence (essentially, a slope).  Therefore, any… Read more »

This page captures some of the work flow gestures in the Compensation user interfaces in FlowJo. For more details, consider looking at our Compensation Tutorial or Work Flow. Assigning Control Tubes to the Compensation Group: This should happen automatically as you add data. Samples will be placed in the “compensation” group if they contain the phrase… Read more »

The univariate cell cycle platform produces a number of statistics that can be used to summarize the modeling results.  This page is under construction; stay tuned for FlowJo Version 10 with Cell Cycle. FlowJo univariate Cell Cycle analysis can produce an array of statistics, which are shown in the upper portion of the model window, as… Read more »

This page contains suggestions for improving the fit of difficult to model cytometric data. Preprocessing Removing doublets, dead cells, and debris will improve the condition of data. Whatever steps you typically follow to do this can be applied to cell cycle data.  Some common methods for doing this are: Doublets can be removed by plotting… Read more »

There are four controllers for the 3D Viewer: Plot, Top Bar Controls, Parameters and Color   Plot From the Plot, set the parameters for X, Y and Z axes and assign a color if wanted. Setting Size: event size will scale based on how positive/negative events are for a specified parameter. More positive events will… Read more »

Welcome to FlowJo, a software application with an integrated environment for viewing and analyzing flow cytometric data. The environment is presented as the Workspace, which contains a list of loaded samples (experimental data), statistics, gates, and other analyses, as well as tabular and graphical layouts. The workspace is saved as a FlowJo document on your hard… Read more »