Flow Cytometry Panel Builder

Multicolor flow cytometry with 5 easy steps

With this tool, you can:

  • Create a new immunophenotyping experiment or add antibodies and reagents to an older panel
  • Insert antibodies already used in your experiment
  • View fluorochrome spectrums to quantify emission spectral overlap
  • Export an excel document with your antibody choices or directly order

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Getting started with the flow cytometry panel builder tool

Choosing the optimal combination of fluorochromes can be simplified with a guided method. The Invitrogen Flow Panel Builder offers a customizable panel building process to fit your flow cytometry experimental needs, whatever your experience level.

5 step video  Staining indexes  Immune cell markers  Relative antigen density  Tips and tricks videos

Video: how to use the panel builder

Watch the video to learn how to use the Invitrogen Flow Cytometry Panel Builder to build your next flow cytometry panel in 5 easy steps.

5 steps of the flow cytometry panel builder

Following 5 simple steps, anyone can design a flow cytometry panel. Whether they are new to flow cytometry or experts in the field, the panel builder can help.

Cytometer configuration

Knowing your cytometer’s configuration is the first step in panel design. Use the drop-down menu containing over 70 instruments to select your cytometer.

Step 1. Flow Cytometer configuration
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If the bandpass filters shown do not match what is in the instrument you will use, simply click the “edit cytometer settings” to adjust the lasers, channels, or bandpass filters as necessary.

Step 1. Edit Flow Cytometer configuration
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If your cytometer is not found, simply enter the configuration manually. Select your lasers and set up the channels and filters as necessary for your cytometer.

Step 1. Flow Cytometer manual entry
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Antigen selection

Are you designing this panel with a key antibody conjugate that you already have in your lab and will not need to purchase? If so, click yes and enter the antigen name, fluorochrome, and intended channel. Then click “add to panel.”

Step 2. Key antibody conjugate that you already have
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Now begin adding the other antigens by first selecting your target species from the drop-down menu. Type in the antigens you need, clicking “add another antigen” until all of your antigens are listed.


If you would like to specify a specific clone, simply use the advanced options to select the desired clone.

Want to assign something to a dump channel? Open the advanced options for the antigen and move the slider to the right, to select yes. This will allow you to assign more than one antigen to this channel.


Don’t forget the viability dye!  Select either the fixable or non-fixable option.


When you are done, click on the Next Step button.

Fluorochrome selection

Fluorochrome selection is guided by the spectral information of each fluorochrome. This step allows you to visualize the spectra of selected fluorochromes across the top of the page as you select fluorochromes for each antigen shown on the left.

Before any selection is made, the number of available channels for each antibody is shown. With each antigen selection, another spectrum will show at the top of the page. A matrix view allows you to see the antigens listed in the rows and with the channels shown in the columns.

Step 3. Fluorochrome selection matrix view
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Begin making fluorochrome selections. Start with the top row which lists the antigens with the fewest fluorochrome options available. Work down the table to the antigens with the most fluorophore options on the bottom. To guide you in fluorochrome selection, spectral information is provided. In general, the least spectral overlap is best.

Continue selecting your options to match all antigens with a fluorochrome. When done, check that your choices will work for your instrument by clicking on the SpectraViewer button.

Step 3. Open SpectraViewer view
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The full spectra of all fluorochromes per laser will show and be labelled. View the estimated light captured by the bandpass filters in your instrument. Be sure to check the theoretical spillover values for issues.

If the fluorochrome you want to select is not listed, simply click to add a placeholder fluorochrome.


Enter your fluorochrome, click add and select to add it to your panel.

Placeholder fluorochromes can be used at any time, even if no other fluorochromes are listed. Simply click on the plus sign, and then enter and select your fluorochrome of choice. When you click on the SpectraViewer link you will be able to visualize your selected fluorochrome.

Step 3. Plus for Placeholder fluorochrome
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Product selection

Select the products and packaging sizes that you want. If you didn’t specify a clone earlier, a variety of clones will be displayed.

Step 4. Product Selection clone and package
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Need additional information to help you decide? Click on an image in the product selection listing to enlarge it. Clicking on the product name will open the product data page in a separate window.

Panel summary

After completing product selection, step 5 allows you to review all of your selected antibodies per laser type and the resulting excitation spectra to be captured by the filter sets of your cytometer.


Want to review the spillover matrix? Simply click the SpectraViewer button to see the matrix.

Not satisfied? Want to change something? You can return to editing by clicking the “Edit panel” button.  Alternatively, you can click on the progress bar at the bottom of the screen to move back to a different step. At any time in the process, once a step has been completed, you may click on a step in the progress bar to return to it. 

Once you have reviewed and are satisfied, you are almost done. Be sure to save your flow cytometry panel and give it a name. There are also options to export the panel design data as a spreadsheet or to download a PDF for printing.

Lastly, simply add the flow cytometry panel that you designed to your cart for purchase. If you are outside the US, the pricing in the Panel Builder will show in your country’s currency, and when you click the “add all to cart” button, the correct pricing and currency for your country will also show in the cart summary field.

Invitrogen Flow Cytometry Panel Builder FAQs

  1. Can I go back a step without losing the work I did?
    • Yes, the previous work is saved.
  2. My marker isn’t showing up under step 2 of antigen, but I see it in the catalogue. How can I remedy this?
    • Select your target species first, and then type your antigen.
  3. How do I share my panel with my lab manager?
    • Export the spreadsheet found on step 5.
  4. What do the colorful dots indicate in the “Fluorochromes” step?
    • The dots indicate the number of fluorochromes that Thermo Fisher Scientific has available in each channel on the cytometer you have chosen.
  5. My cytometer does not use a standard configuration. How can I make changes to one in the dropdown?
    • Select a cytometer from the dropdown menu and then select the “Edit cytometer settings” link to modify the configuration as needed.
  6. I can’t find my cytometer in the dropdown. Can I build one?
    • Yes, you can define a new cytometer using the “Enter your cytometer manually” link below the cytometer dropdown menu.
  7. I do not order products through thermofisher.com. What other endpoints are available to me?
    • There are both PDF (printable) and CSV (spreadsheet) exports available in the summary step for you to take away for reference and ordering purposes.
  8. I plan to use antibodies that are not from Thermo Fisher Scientific. How can this Panel Builder be useful to me?
    • Step 2 allows for antibodies you already purchase or from outside Thermo Fisher Scientific. If you are undecided about which format you want for something, you can add the antigen name in the “Antibodies you need” section and then choose a placeholder fluorochrome in the following step. Both will help you keep track of channels that are reserved for reagents that you do not plan to buy from Thermo Fisher Scientific.

Common fluorochrome brightness

Fluorophores emit light with varying levels of brightness (Figure 2). When choosing fluorochromes on the panel builder, we suggest:

  • Have a staining index for your specific flow cytometer. A staining index can be provided as a chart or table from a manufacturer who tested the same clone with different conjugates on their instrument. It is also possible to create a staining index with flow capture beads. For example, Figure 2 shows a staining index of the most popular fluorochromes analyzed on the Attune NxT Flow Cytometer. Each flow cytometer has different lasers, filters, and detectors that can influence the signal observed from a marker conjugated to a fluorochrome.
  • When designing a multicolor experiment, choosing only very bright fluorochromes may result in spillover and can dampen the signal of a marker.
  • Examine the mean fluorescence intensity for each fluorochrome and antibody clone to compare brightness. These can be found in product data sheets.

Want to know more about a staining index? Need the staining index for the BD™ LSR II Flow Cytometer? Find it in our Flow Cytometry Panel Design: Basics

Chart showing more than 40 flurochromes in rank order of mean stain index
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Figure 2. Average stain index of fluorochrome conjugated to CD4 and analyzed on the Attune NxT Flow Cytometer.

Strategies for identifying immune cell markers

Each channel on your flow cytometer can report on the presence of a marker when it is bound by a fluorochrome-conjugated detection molecule. Many publications give lists of markers for various detection strategies, but in general we recommend:

  • Employing a strategy to detect a combination of positive, negative, and functional markers to identify a cell. More markers give a more comprehensive analysis of a cell population and provide more confidence in a cell identification.
  • Accounting for gene and protein expression changes when cells are stimulated or isolated from different sources.
  • Using Optimized Multicolor Immunofluorescence Panels (OMIPs) to aid in the design or expand a panel. Each publication provides (1) information about the cell populations, antigen density, and marker co-expression; (2) optical configuration of the instrument, including excitation wavelengths and emission filters available; (3) antibody characteristics; (4) fluorophore characteristics.

Looking for markers to detect your cells? We have a guide for human and mouse cellular markers.

Illustration of 4 immune cell types - Natural killer cell
Illustration of 4 immune cell types - Treg
Illustration of 4 immune cell types - B cell
Illustration of 4 immune cell types - T cell

Figure 3. Immune cells may be identified by viability dyes in combination with labeled antibodies targeted to markers that are specific to each cell.

Relative antigen density for common immune cell markers

Choosing an antibody should be based on both antigen abundance and fluorochrome brightness to minimize compensation and help ensure good resolution of cell populations. We advise:

  • Using antigen density tables as a guide (see below for examples of antigen density for popular T and B cell markers). Gene expression levels may vary depending on cell source, stimulation, and protocols used for fixation.
  • Dim fluorochromes to detect highly expressed proteins and bright fluorochromes to detect less-abundant proteins.
  • Use flow cytometry compensation beads to help determine the specific density of your antigen. Internet-accessible databases can also help to find RNA expression levels.

Table 1. Antigen density for popular T cell markers.

Targets Typical expression levels
CD3 High
CD4 High
CD8 High
CCR7 Low to medium
IL-2 Medium
IFN gamma Medium to high
Phospho-CD247 (CD3z) Y142 Medium to high
CD45RA High
CD45RO Medium to high
CD27 Medium to high
CD28 Medium to high
CD122 Medium to high
CCR4 Low to medium
CD127 Low to medium
CD25 Low to medium
CD132 Low to medium

Table 2. Antigen density for popular B cell markers.

Targets Typical expression levels
CD19 Low to medium
IgM Low
CD20 High
CD34 High
CD25 High to medium
CD27 Low
CD138 Low
CXCR4 High to medium
IL-10 High to medium

Quick tips and tricks for your best panel

R&D scientist Natalie Oxford share her learnings for a flow cytometry panel that can help you get published.

Tip 1: Minimize spill-over by using the correct and separate channel

Any time you have markers that you know will be co-expressed on your cells of interest, make sure to space them out into separate channels. If you will need to use any adjacent channels, that's where you would put any markers that are mutually exclusive so that they'll still be easy to distinguish.

Tip 2: Intracellular targets need special buffer for fixation and permeabilization for staining

You'll also want to keep in mind the buffer that you're using to fix and permeabilize your cells, as we have several options. When you're looking at cytoplasmic targets, what the buffer is appropriate may not be the same as when you're looking at nuclear targets, because you want to make sure that you still have access to your antigens without over-fixing your epitopes.

Tip 3: Viability dyes are required to find live cells

A third tip I wanted to share with you is to always include a viability dye in your staining panel. This will help eliminate any false positives that are caused by dead cells or debris, because those can be sticky. You have a lot of options for choosing a viability dye, so you don't need to design your panel around them. You can build out the rest of your panel and optimize your core markers, and then fit in a viability dye in an empty channel.

Tip 4: Save your bright fluorochromes for dim targets

As you're building out your basic panel and you want to incorporate some more antigens, make sure you're keeping the density of your antigen expression in mind. So if you have antigens with low or unknown expression, those would be ones that you want to assign to your brightest dyes, such as PE or APC.

Tip 5: Try to combine negative markers in one channel (dump channel) to save space on your panel

A helpful trick when you want to exclude a lot of cell types at once without having to suck up multiple channels for that would be to use a dump channel. This is where you're placing all the antibodies that identify your cells that are not of interest into the same channel with the same fluorochrome, and then those can be easily gated out and all of the cells negative for the dump channel would be those that you use for your analysis going forward.

Looking for quick tips and tricks? Find it in our Flow Cytometry Panel Design: Basics

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.
Brilliant Violet and PE CF dyes are subject to proprietary rights of Becton, Dickinson and Company.
CyTM is a trademark of Amersham Biosciences Corp. Cy dyes are subject to proprietary rights of Amersham Biosciences Corp and Carnegie Mellon University and are made and sold under license from Amersham Biosciences Corp only for research and in vitro diagnostic use.