Cytometry and Antibody Technology

Panel Design

Traditional Flow Cytometry

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Panel Design Overview

Before designing a panel, you should gather some information:

  • A list of markers for your panel
  • Expression level of markers on your cells of interest (high/low/unknown)
  • A rough gating strategy
  • Determine which instrument you are using and which fluorophores are best for that instrument

Then you can begin to assemble your panel:

  • Spread out your markers evenly over the lasers (i.e. don’t use 5 violet laser fluorophores for a 6-color panel)
  • Assign highly expressed markers to dim fluorophores and markers with low or unknown expression to bright fluorophores

Check out this blog post to learn about common panel design mistakes that lead to bad data. Flow Basics 2.0 is a 5-part training course that covers the practical steps for designing and executing a flow cytometry experiment. The third is below and covers steps for successful panel design. The full course can be found within the Resources Library.

External Websites to support your panel design needs

Registration may be required

Cytek Cloud

Cytek’s online platform offers a spectral analyzer and a panel design tool. You can also create your SpectroFlo experiment that you can then upload to the acquisition software on our instruments.

Easy Panel Experiment Design Platform

Our recommended panel design tool. Automatically pairs your markers with the most appropriate fluorophores by optimizing the complexity and global similarity index.


Our instruments are listed on Fluorofinder. The website will guide you through the panel design steps: enter your marker, target species, antigen density, etc. The result is a list of available antibodies paired with fluorophores from various manufacturers.


BenchSci is an AI-Assisted antibody selection tool. Simply enter the desired antibody and you get a list of figures and publications related to that antibody.


CiteAb provides a way to choose reagents by reviewing the scientific literature.


Optimized Multicolor Immunofluorescence Panel (OMIP) is a special peer-reviewed Cytometry Part A publication type that reports on newly designed and optimized multicolor panels for flow cytometry, fluorescence microscopy, image cytometry, and other polychromatic fluorescence-based methods. OMIPs are aimed: (1) to alleviate the development time for researchers in need of the same or highly similar panels, (2) to provide a starting point for the creation of novel OMIPs, and (3) to give the developers of the panels credit via citation or the publication.

Spectra Viewers
Other Useful Information
Antibody Fixation Consideration (Thermofisher)

List of popular antibody clones and how epitopes are impacted by fixation.

Antibody Fixation Consideration (BioLegend)

List of popular antibody clones and how epitopes are impacted by fixation.

Phospho-Buffer Consideration (ThermoFisher)

List of popular antibody clones and how epitopes are impacted by Phospho-buffers.

PhosphoFlow Buffer Compatibility (BD Biosciences)

Compatibility of various antibody clones in multiple PhosphoFlow buffers.

Enzyme Explorer for Tissue Dissociation (Millipore Sigma)

Guidance for selecting tissue digestion enzymes.

Essential Markers for Phenotyping (BioLegend)

Essential markers for identifying immune cell populations in human and mouse.