Using FluoroFinder

Update!  The team at FluoroFinder has created this step-by-step tutorial video to help you build panels!  Check out the video or the written tutorial below to get started with FluoroFinder!


The Syracuse flow core has recently acquired the services of FluoroFinder, an application that will allow our users to build interactive fluorophore panels customized around the laser/filter configurations of the instruments available in the core. The FluoroFinder service will be a great asset to any flow core user, regardless of your level of experience with flow cytometry or cell sorting, and has the potential to simplify the process of choosing appropriate fluorophores for an experiment. The application has a variety of dyes, stains, fluorescent proteins, and conjugated antibodies from several commonly used companies and also provides the option to add your own fluorophore (if, for example, you have your own conjugated antibody, or a stain is not available). It also provides the ability to search by category if you are unsure what to use (if, for example, you would like to use a viability dye, but aren’t sure what is available and compatible). Here we will provide a step-by-step tutorial for using the FluoroFinder service for building your flow cytometry panels.

  1. Go to
  2. Choose the instrument you are planning to use
    1. Choose the Accuri C6 for flow cytometry
    2. Choose the Aria II or cell sorting
  3. Clicking on the instrument will take you to its specific laser and filter configurations. This page will also list suggested (commonly used) colors/fluorophores for each filter channel. If you move your mouse to the right of each fluorophore, you will find the Edit button, which will allow you to change the fluorophore in each channel. Use this if you already know what changes you would like to make. There are three buttons near the top of the page that can be clicked.
    1. The first is Panel Professor
      1. Clicking this will give you an overview of options to configure the panel
    2. The second is Color Rank
      1. Clicking this will rank the intensity of the fluorophores on the screen
    3. The third is Continue
      1. Clicking this will take you to the next screen
    4. Clicking Continue will take you to the second screen (Markers), where you will be able to select all the fluorophores you would like to use in your panel. If you are using the C6, you can choose 4 colors; if you are using the AriaII, you can choose 13 colors. There are a couple options for choosing colors here:
      1. If you know the fluorophore you would like to use, you can enter in the box under the column Markers. You can choose your target species, host, isotype, and clone as appropriate in the following columns.
      2. If you aren’t sure which fluorophore you would like to use, you can search by category. For example, if you know you are looking for a viability dye but you aren’t sure what is available, you can simply type ‘viability dye’ into the box under the Markers column and leave the other columns blank.
      3. When you have finished making your fluorophore selections, click
    5. Based on your selections on the previous screen, FluoroFinder will now give you options for fluorophores compatible with the flow core instrument you want to use. There are several options at the top of the screen you should consider for use:
      1. Include equivalent colors will include fluorophores similar to the one(s) you selected on the previous screen.
      2. Show colors that fit will show only colors compatible with the instrument you selected in the beginning
      3. Include colors not in our catalog will allow you to view colors that are not listed in the FluoroFinder system. This will be relevant if you added your own fluorophore
      4. Show fluorescent proteins will, as the name says, show fluorescent proteins that are compatible with each channel

Based on the fluorophores you selected in the previous screen (for example, if you searched for viability dyes), one or more columns will appear to indicate which items fall within your search parameters. FluoroFinder will divide the available fluorophores into the appropriate channels on the cytometer (based on their respective excitation and emission spectra).

  1. You can hover over each available fluorophore to view the intensity. Each will also have a number in parentheses beside it. This number indicates the number of products listed in the FluoroFinder directory. Clicking on the fluorophore will bring up a listing that will tell you from what supplier(s) it is available, as well as the price.
  2. Once you select a particular fluorophore for each channel, you cannot select another fluorophore for that channel.
  3. Make all of your selections, and then click Continue at the top of the screen. Remember that you can save the panel at any time (also at the top of the screen). The next screen will show your completed panel with your selected fluorophores in their respective channels on the cytometer of your choice.
  4. This is the final step of the building process, but you still have a few options:
    1. You can start over by choosing Build Another Panel.
    2. You can choose Save Panel for later review.
    3. You can choose Email Panel to send the email to yourself or another for consideration.
    4. You can choose Send for Review to send the panel to facility operator Grace Altimus for review or questions.
    5. You can also Print or generate a PDF of the panel.
  5. You may use the service without registering, or you can register with FluoroFinder for a free account. If you have any questions about the service or about building a panel, please contact the operator. We hope you will find this to be a useful application and that it will benefit experiments in the core. If you use FluoroFinder, please give us your thoughts and feedback!