Compensation FAQ This page will help acquaint you with the various ways to interact with Compensation Matrices in FlowJo. For your convenience, this document is broken into chapters. Note, Compensation should always be preceded by scaling your data appropriately. Poorly scaled data will effect downstream compensation, so get into the habit of adjusting transforms through… Read more »

This page describes the compensation window. To open this window, click on your Compensation group to select it, then click the tool menu tab and select Compensation: This will open the main Compensation Window: This is a complex window, let’s examine it one part at a time. The top part of the window deals with… Read more »

The following papers are great to learn more about compensation: Spectral Compensation for Flow Cytometry: Visualization Artifacts, Limitations, and Caveat. Mario Roederer, Cytometry 45:194 –205 (2001) A practical approach to multicolor flow cytometry for immunophenotyping. Baumgarth, Roederer. Journal of Immunological Methods 243 (2000) 77–97 Seventeen-colour flow cytometry: unravelling the immune system. Perfetto, Chattopadhyay and Roederer. Nature Review, Immunology Vol. 4… Read more »

Starting with version 10 of FlowJo, there is a new interface for viewing compensation matrices – the Matrix Editor. This page describes the Matrix Editor. The matrix editor window can be accessed in two ways: 1) by double-clicking the compensation badge from the workspace window (any compensated sample has this badge next to the sample in… Read more »

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 »