Skip to main content

Principles of Advanced Flow Cytometry: A Practical Guide

  • Protocol
  • First Online:
T-Cell Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2580))

Abstract

Recent advances have revolutionized the oldest high-throughput single-cell analytical tool, flow cytometry. Fluorescent analyzers and sorters with up to seven lasers and the potential to detect up to 50 parameters are changing the way flow cytometry is used, but old school practices which are inadequate for new technologies remain alive. This chapter summarizes recent advances, explains the most salient new features and offers a step-by-step guide to develop and successfully execute high-dimensional fluorescent flow cytometry experiments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Bagwell CB, Adams EG (1993) Fluorescence spectral overlap compensation for any number of flow cytometry parameters. Ann N Y Acad Sci 677:167–184. https://doi.org/10.1111/j.1749-6632.1993.tb38775.x

    Article  CAS  PubMed  Google Scholar 

  2. Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, Pavlov S, Vorobiev S, Dick JE, Tanner SD (2009) Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem 81:6813–6822. https://doi.org/10.1021/ac901049w

    Article  CAS  PubMed  Google Scholar 

  3. Behbehani GK, Bendall SC, Clutter MR, Fantl WJ, Nolan GP (2012) Single-cell mass cytometry adapted to measurements of the cell cycle. Cytometry A 81:552–566. https://doi.org/10.1002/cyto.a.22075

    Article  PubMed  PubMed Central  Google Scholar 

  4. Brummelman J, Haftmann C, Núñez NG, Alvisi G, Mazza EMC, Becher B, Lugli E (2019) Development, application and computational analysis of high-dimensional fluorescent antibody panels for single-cell flow cytometry. Nat Protoc 14:1946–1969. https://doi.org/10.1038/s41596-019-0166-2

    Article  CAS  PubMed  Google Scholar 

  5. Grégori G, Patsekin V, Rajwa B, Jones J, Ragheb K, Holdman C, Robinson JP (2012) Hyperspectral cytometry at the single-cell level using a 32-channel photodetector. Cytometry A 81:35–44. https://doi.org/10.1002/cyto.a.21120

    Article  PubMed  Google Scholar 

  6. Habbersett RC, Naivar MA, Woods TA, Goddard GR, Graves SW (2007) Evaluation of a green laser pointer for flow cytometry. Cytometry A 71:809–817. https://doi.org/10.1002/cyto.a.20454

    Article  PubMed  Google Scholar 

  7. Lansdorp PM, Smith C, Safford M, Terstappen LW, Thomas TE (1991) Single laser three color immunofluorescence staining procedures based on energy transfer between phycoerythrin and cyanine 5. Cytometry 12:723–730. https://doi.org/10.1002/cyto.990120806

    Article  CAS  PubMed  Google Scholar 

  8. Li W, Vacca G, Castillo M, Houston KD, Houston JP (2014) Fluorescence lifetime excitation cytometry by kinetic dithering. Electrophoresis 35:1846–1854. https://doi.org/10.1002/elps.201300618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Liechti T, Weber LM, Ashhurst TM, Stanley N, Prlic M, Van Gassen S, Mair F (2021) An updated guide for the perplexed: cytometry in the high-dimensional era. Nat Immunol 22:1190–1197. https://doi.org/10.1038/s41590-021-01006-z

    Article  CAS  PubMed  Google Scholar 

  10. Maecker HT, Trotter J (2006) Flow cytometry controls, instrument setup, and the determination of positivity. Cytometry A 69:1037–1042. https://doi.org/10.1002/cyto.a.20333

    Article  PubMed  Google Scholar 

  11. Mair F, Tyznik AJ (2019) High-dimensional Immunophenotyping with fluorescence-based cytometry: a practical guidebook. Methods Mol Biol 2032:1–29. https://doi.org/10.1007/978-1-4939-9650-6_1

    Article  CAS  PubMed  Google Scholar 

  12. Barteneva NS, Vorobjev IA (2016) Imaging flow cytometry, 1st edn. Humana Press. https://doi.org/10.1007/978-1-4939-3302-0

    Book  Google Scholar 

  13. Nguyen R, Perfetto S, Mahnke YD, Chattopadhyay P, Roederer M (2013) Quantifying spillover spreading for comparing instrument performance and aiding in multicolor panel design. Cytometry A 83:306–315. https://doi.org/10.1002/cyto.a.22251

    Article  PubMed  PubMed Central  Google Scholar 

  14. Park LM, Lannigan J, Jaimes MC (2020) OMIP-069: forty-color full spectrum flow cytometry panel for deep immunophenotyping of major cell subsets in human peripheral blood. Cytometry A 97:1044–1051. https://doi.org/10.1002/cyto.a.24213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Roederer M, Murphy RF (1986) Cell-by-cell autofluorescence correction for low signal-to-noise systems: application to epidermal growth factor endocytosis by 3T3 fibroblasts. Cytometry 7:558–565. https://doi.org/10.1002/cyto.990070610

    Article  CAS  PubMed  Google Scholar 

  16. Schwann T (1839) Mikroskopische Untersuchungen ueber die Uebereinstimmung in der Struktur und dem Wachstum der Thiere und Pflanzen (Verlag van Sanderschen Buchhandlung)

    Google Scholar 

  17. Wade CG, Rhyne RH Jr, Woodruff WH, Bloch DP, Bartholomew JC (1979) Spectra of cells in flow cytometry using a vidicon detector. J Histochem Cytochem 27:1049–1052. https://doi.org/10.1177/27.6.110874

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors wish to acknowledge Karen Wolcott (CCR/LGI Flow Core) for help with training on the Sony ID7000 spectral analyzer, Jeff Clapper (Sony Biotechnology) for helpful discussions and insight in spectral flow cytometry and Hidehiro Yamane, and Mariah Lee (CCR/LCMB, NCI, NIH) for providing unpublished data in Figs. 6 and 7 for the comparison of conventional and spectral flow cytometry analyses.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ferenc Livák .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Siddiqui, S., Livák, F. (2023). Principles of Advanced Flow Cytometry: A Practical Guide. In: Bosselut, R., Vacchio, M.S. (eds) T-Cell Development. Methods in Molecular Biology, vol 2580. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2740-2_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2740-2_5

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2739-6

  • Online ISBN: 978-1-0716-2740-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics