New approaches to fluorescence compensation and visualization of FACS data.

The Fluorescence Activated Cell Sorter (FACS) is an invaluable tool for clinicians and researchers alike in phenotyping and sorting individual cells. With the advances in FACS methodology, notably intracellular staining for cytokines, transcription factors and phosphoproteins, and with increases in the number of fluorescence detection channels, researchers now have the opportunity to study individual cells in far greater detail than previously possible. In this chapter, we discuss High-Definition (Hi-D) FACS methods that can improve analysis of lymphocyte subsets in mouse and man. We focus on the reasons why fluorescence compensation, which is necessary to correct for spectral overlap between two or more fluorochromes used in the same staining combination, is best done as a computed transformation rather than using the analog circuitry available on many flow cytometers. In addition, we introduce a new data visualization method that scales the axes on histograms and two-dimensional contour (or dot) plots to enable visualization of signals from all cells, including those that have minimal fluorescence values and are not properly represented with traditional logarithmic axes. This "Logicle" visualization method, we show, provides superior representations of compensated data and makes correctly compensated data look correct. Finally, we discuss controls that facilitate recognition of boundaries between positive and negative subsets.