green, blue, red, yellow and pink color laser lights intersecting at multiple points

Advances in both flow cytometry reagents and instrumentation allow researchers to run increasingly complex multicolor experiments. One of the biggest challenges in multiparameter flow cytometry is selecting the right combination of fluorophores and antibody conjugates so that the need for compensation and spillover adjustments is kept to a minimum while the quality and accuracy of the data are not compromised. In this section you will find educational resources and tools to help you design and execute multicolor flow cytometry experiments, including panel design tool, articles, application notes, on demand webinars, and more.

Panel design and multicolor flow cytometry features

Flow cytometry panel design tool

Screen view of the Thermo Fisher Scientific flow cytometry panel design tool with viability dye and 2 antibody options for the violet and the blue lasers

Flow Cytometry Panel Builder

This online tool guides you through flow cytometry panel design, providing a simplified, customizable experience to fit your flow cytometry panel design needs.


Panel design and multicolor flow cytometry learning resources

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Type Title Categories
Application note (2015) Attune NxT Flow Cytometer for 6-color immunophenotyping analysis of stained human whole blood using a no-lyse, no-wash protocol, with no compensation Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Detection of murine regulatory T cells on the Attune NxT Flow Cytometer Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Multiparameter analysis of murine regulatory T cells and dendritic cells with the Attune NxT Flow Cytometer Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015) Ten-parameter immunophenotyping of human lysed whole blood with the Attune NxT Flow Cytometer allows identification of multiple T cell subsets and myeloid cells Attune NxT, flow cytometer, immunophenotyping, multicolor flow cytometry
Application note (2015)  13-parameter immunophenotyping of human lysed whole blood with the Attune NxT Flow Cytometer allows for the identification of B cells, NK cells, multiple T cell subsets and myeloid cells  Alexa Fluor, antibodies, Attune NxT, compensation, flow cytometer, fluorescent dyes, immunophenotyping, multicolor flow cytometry, nanocrystals, Qdot
BioProbes article (2017) T lymphocyte immunophenotyping—14-color flow cytometry panel featuring Super Bright antibody conjugates antibodies, Attune NxT, immunology, immunophenotyping, multicolor flow cytometry, Super Bright
BioProbes article (2016) Optimized multicolor immunofluorescence panels (OMIPs)—Jump-start your experimental design with published antibody and reagent panels flow cytometry, fluorescence, immunophenotyping, multicolor flow cytometry
BioProbes article (2015) Flow cytometry panel design: The basics flow cytometry, fluorescence, multicolor flow cytometry
BioProbes article (2010) Optimal pairing of dyes and antibodies for flow cytometry antibodies, fluorescence, multicolor flow cytometry, particles Qdot
BioProbes article (2007)  Simultaneously visualize surface and intracellular markers  antibody labeling, cell fixatives, flow cytometry, fluorescent dyes, sample preparation, Zenon
BioProbes article (2006)  Multicolor immunodetection using the violet laser  Alexa Fluor, antibody labeling, flow cytometry, fluorescent dyes, immunophenotyping, multicolor flow cytometry, nanocrystals, Qdot
Scientific Poster (2017)  T-lymphocyte immunophenotyping: 14-color flow cytometry panel design using the Attune NxT Flow Cytometer and Super Bright fluorescent dyes  antibodies, Attune NxT, fluorescent dyes, immunophenotyping, multicolor flow cytometry, particles, Super Bright
Scientific poster (2009)  A comparative study of 25 different CD4 conjugates  Alexa Fluor, antibodies, fluorescent dyes, immunophenotyping, multicolor flow cytometry, nanocrystals, Qdot
CYToMORE lecture video (2016) Heterogeneity of tumour-infiltrating leukocytes: implications for adoptive cell transfer immunotherapy 
Presented by Enrico Lugli, Humanitas Clinical and Research Center, Italy
flow cytometry, immunology, immunophenotyping
Tutorial video Molecular Probes Tutorial Series—Anatomy of Fluorescence Spectra  absorbance, emission, excitation, spectra
Tutorial video Molecular Probes Tutorial Series—Introduction to Flow Cytometry  flow cytometer calibration, multicolor flow cytometry
Tutorial video Molecular Probes Tutorial Series—Introduction to Fluorescence  flow cytometry, fluorescence imaging
Tutorial video Molecular Probes Tutorial Series—Overview of Filters and Light Sources  emission, excitation, filters, light cubes, light sources
Webinar Basics of flow cytometry, Part I: Gating and data analysis 
An introduction to fluorescence, this presentation covers the following topics: the principle of the flow cytometry platform, the basic components of a flow cytometer, how to interpret a dye excitation/emission spectrum, how data is displayed, basic gating demonstration, and common statistics and terminology used in flow cytometry.
flow cytometry data, flow cytometry set up, multicolor flow cytometry
Webinar Basics of multi color flow cytometry panel design 
With the proliferation of new fluorescent dyes, as well as instruments that can detect 18 or more parameters multicolor flow cytometry has become more popular and more accessible than ever. This webinar presented by Dr. Holden T. Maecker at Stanford University will discuss the caveats of good panel design, including:
  • Rules for designing panels
  • Examples and practical application of these rules
  • Controls and standardization
  • Relevance of panel design to new mass cytometry platforms
antibodies, compensation, multicolor flow cytometry

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.