Flow Cytometry Panel Builder

Build your flow cytometry panel in 5 easy steps

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

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.

Step 1. 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.

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.

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 2. 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.”

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.


Step 3. 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.

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.

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 4. 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.

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.


Step 5. 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.