Spectral compensation for flow cytometry: visualization artifacts, limitations, and caveats

Cytometry. 2001 Nov 1;45(3):194-205. doi: 10.1002/1097-0320(20011101)45:3<194::aid-cyto1163>3.0.co;2-c.


Background: In multicolor flow cytometric analysis, compensation for spectral overlap is nearly always necessary. For the most part, such compensation has been relatively simple, producing the desired rectilinear distributions. However, in the realm of multicolor analysis, visualization of compensated often results in unexpected distributions, principally the appearance of a large number of events on the axis, and even more disconcerting, an inability to bring the extent of compensated data down to "autofluorescence" levels.

Materials and methods: A mathematical model of detector measurements with variable photon intensities, spillover parameters, measurement errors, and data storage characteristics was used to illustrate sources of apparent error in compensated data. Immunofluorescently stained cells were collected under conditions of limiting light collection and high spillover between detectors to confirm aspects of the model.

Results: Photon-counting statistics contribute a nonlinear error to compensated parameters. Measurement errors and log-scale binning error contribute linear errors to compensated parameters. These errors are most apparent with the use of red or far-red fluorochromes (where the emitted light is at low intensity) and with large spillover between detectors. Such errors can lead to data visualization artifacts that can easily lead to incorrect conclusions about data, and account for the apparent "undercompensation" previously described for multicolor staining.

Conclusions: There are inescapable errors arising from imperfect measurements, photon-counting statistics, and even data storage methods that contribute both linearly and nonlinearly to a "spreading" of a properly compensated autofluorescence distribution. This phenomenon precludes the use of "quadrant" statistics or gates to analyze affected data; it also precludes visual adjustment of compensation. Most importantly, it is impossible to properly compensate data using standard visual graphical interfaces (histograms or dot plots). Computer-assisted compensation is required, as well as careful gating and experimental design to determine the distinction between positive and negative events. Finally, the use of special staining controls that employ all reagents except for the one of interest (termed fluorescence minus one, or "FMO" controls) becomes necessary to accurately identify expressing cells in the fully stained sample.

MeSH terms

  • Artifacts*
  • Calibration
  • Flow Cytometry / methods*
  • Fluorescent Antibody Technique / methods
  • Humans
  • Immunophenotyping / methods
  • Leukocytes, Mononuclear / immunology
  • Models, Biological
  • Spectrum Analysis
  • Statistics as Topic