Tools and Protocols

We offer several solutions in our facility to help with experiments, including design support, storage solutions, and analysis assistance.


The flow cytometry facility administers the UTSW site license for FlowJo analysis software, which allows us to offer a heavily discounted version of the software to our users. To participate in this program, you must have a CRI PPMS account and be affiliated with UT Southwestern. To obtain a license for your computer, place the order through CRI’s PPMS. We also have two computers available to utilize the FlowJo software.  Our flow cytometry experts are also available to help analyze data.

Spectral Viewer

Several flow cytometry companies, including BD Biosciences and ThermoFisher Scientific, have created fluorochrome spectral viewers to facilitate panel design and to predict compensation values. These online tools are designed to aid customers in understanding important principles, dependencies, and relationships involved in selecting fluorochromes for multicolor flow cytometry. Users of these tools should ultimately rely on their own judgment when selecting fluorochromes for multicolor panels and experiments.

Panel Designer

One difficult task that people encounter when they start making multicolor flow cytometry panels is the process of finding antibodies and determining which fluorochromes to use for our instruments. Our facility recommends using Fluorofinder to help you with this task.

To set up a Fluorofinder account:

  1. Go to
  2. Create an account if you want your panel to be saved.
  3. Select the instrument you want to use and follow the instructions.


Cytobank provides a turnkey storage solution for your flow cytometry data. Cytobank allows researchers to manage, search, and analyze their FCS files over the web. The analysis system is designed to incorporate annotations and make it easier to create figures for lab meetings, publications, or sharing. Cytobank also facilitates discussions about flow cytometry across and within groups. Users can share experiment data and details quickly and easily through the web. Collaborators can start with the result and drill down to the underlying single-cell data.