Moody Foundation Flow Cytometry


Frances Moody-Dahlberg visits the CRI’s Flow Cytometry Facility

The Moody Foundation Flow Cytometry Facility, located within CRI, is a shared resource laboratory (SRL) committed to providing cutting-edge flow cytometry services to scientists at CRI, UT Southwestern and other institutes. The facility is named after the Moody family, who donated $2.5 million to renovate, staff and buy equipment for CRI’s Flow Cytometry Facility in 2013.

The facility offers state-of-the-art analytical cytometry and high-speed sorting either in an investigator-operated format or facility staff assisted format. Our instrumentation is compatible with a wide variety of flow cytometry applications. We also offer training for research personnel interested in learning how to design flow cytometry experiments, operate the instrumentation and analyze data.

We provide several core services, including:

  • Experimental design
  • Protocol development
  • Sample staining
  • Instrument operation
  • Data analysis
  • Graphical production
  • Sample Processing as a Service (SpaaS)

The CRI flow cytometry shared facility is equipped with three cell sorters and four cell analyzers.

The three cells sorters include two FACS Aria II SORP and one FACS Aria Fusion SORP, all in a biosafety hood for sorting primary human cells.

The four cells analyzers includes two LSRFortessa with a High Throughput Sampler (plate loader) that provides fully automated rapid sample acquisition and an enhanced dual FSC detection system (PMT + diode) with the ability to detect <0.2 um particles from noise on the SORP version and one special order FACS Canto RUO – 12 parameters – with tubes loader. These instruments operate on a PC-based platform using FACSDiva (version 8) software. Our last addition is the clinical ready instrument FACS Lyric -14 parameters- with universal loader (tubes or plates), which operates on a PC-based platform, using FACSuite software that maximize the accuracy and reproducibility of data over time between instruments – whether at the same site or across the globe.

If you would like to gain access to the facility, please visit CRI PPMS and complete an account creation request. For answers to commonly asked questions and helpful links, please refer to our FAQ.

Introduction to Flow Cytometry

Flow cytometry is a powerful tool for investigating many aspects of cell biology due to its ability to quantitatively analyze individual cells and identify different subpopulations of cells. This makes flow cytometry a valuable tool for cell analysis and cell sorting. Cell features are detected primarily by fluorescence though significant information, such as cell “size” and “granularity”, is also contained in the way light is scattered by the cells. The power of single cell analysis is heightened by the ability to analyze multiple parameters simultaneously. Flow cytometers equipped with the latest technology available, such as those offered in our facility, can also analyze and sort cells at extremely high rates. Applications of flow cytometry include immunophenotyping (using fluorescently labeled antibodies or ligands), measurement of DNA and RNA content for cell cycle analysis, apoptosis, and cell viability. These techniques can be used to answer a diverse range of experimental questions.

Flow cytometry is increasingly being used for preparation of gene libraries by sorting green fluorescent protein (GFP)-marked E. coli transfectants that are directly cloned following sorting. Although flow cytometry is mostly applied to the analysis of cells, it is applicable to any resolvable particle such as chromosomes or bacteria.

Facility Access

The Moody Foundation Flow Cytometry Facility is open to all scientists at CRI, UT Southwestern and other interested institutions.

For untrained users, our staff is available to operate instrumentation Monday through Friday from 9 a.m. to 6 p.m. Facility training courses are available for those interested in being self-operators through flow facility staff members. Training includes mastery of sample preparation, instrumentation and analysis software. Flow cytometers are relative measurement devices, and therefore, outcomes depend on proper setup and use.

For qualified self-operators, the Facility is open 24/7.


Our facility is equipped with three cell sorters and four cell analyzers. To schedule time with our instruments, please visit CRI PPMS.



The FACSCanto RUO is equipped with three lasers (405 nm, 488 nm and 633 nm) that offer simultaneous 12-parameter detection and a FACSLoader. This state-of-the-art instrument offers fixed optical alignment as well as automated compensation and housekeeping routines, making it highly desirable to operate.

FACS Lyric

The FACSLyric is equipped with three lasers (405 nm, 488 nm and 633 nm) that offer simultaneous 14-parameter detection and a FACS Universal Loader. This state-of-the-art instrument combines speed, simplicity and automation to help laboratories be more productive. It is designed to maximize the accuracy and reproducibility of data over time between instruments – whether at the same site or across the globe.


The FACS LSRFortessa SORP is equipped with four lasers (405 nm, 488 nm, 561 nm and 633 nm) that offer simultaneous 18-parameter detection and a High Throughput Sampler (HTS) that provides fully automated and rapid sample acquisition. On one of our systems (LSRFortessa SORP), we have  also included an enhanced dual FSC detection system (PMT + diode) with the ability to detect 0.2 µm particles from noise.

This state-of-the-art instrument offers high power lasers that improve the detection of rare events as well as automated compensation and housekeeping routines, making it highly desirable to operate.

Cells Sorters

FACS Aria II SORP (4 lasers and 5 lasers) / FACS Aria Fusion SOP

The FACSAria II SORP and FACS Aria Fusion SORP offer state-of-the-art features in the most advanced cell sorter on the market. BD FACSAria II SORP and FACS Aria Fusion SORP have air-cooled lasers and fixed-alignment cuvette flow cells, which allow achieving superior fluorescence sensitivity. BD FACSAria delivers high-speed multicolor sorting with digital acquisition rates of up to 20,000 events/second. It is able to achieve sort into two- and four-way bulk sorting devices for a variety of tube sizes and can sort using Automated Cell Deposition Unit (ACDU) to multiwell plates or microscope slides.

Quick reference guides are available for the FACSAria II SORP and FACSAria Fusion SORP. Please review our guidelines for help with sample preparation for sorting.

Two FACSAria II SORP are available in the facility.

Four-laser system (405 nm, 488 nm, 561 nm, 633 nm), which simultaneously collects multiple emission wavelengths (up to 13 fluorescents detectors):

Five-laser system (305 nm, 405 nm, 488 nm, 561 nm, 633 nm) that accommodate up to 17 parameters – 15 colors and 2 scatters:

Also available is one FACSAria Fusion SORP, which is a give-laser system (305 nm, 405 nm, 488 nm, 561 nm, 633 nm) that accommodate up to 20 parameters – 18 colors and 2 scatters.

The three FACSAria (II and Fusion) are in class II biosafety cabinets designed to provide personnel, product and environmental protection from potentially hazardous, aerosolized particulates.

Confocal Microscopy

The Leica TCS SP8 has been designed for confocal microscopy with optimal photon efficiency and high speed. All optical components are matched toward preserving fluorescence photons for image contrast and to improve cell viability in live cell imaging. Backing up this sensitive detection are a high speed scanning system with up to 428 frames per second, large field of view of field number 22 and accelerated Z-stacking by a novel mode for the SuperZ galvanometer called Galvoflow. This suits the instrument for the most demanding samples, highest speed while offering full confocal resolution.

Flow Cytometry Tools


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 for our users. To participate in this program, you must have a CRI PPMS account, be affiliated with UT Southwestern and be able to provide a valid account number for this license for billing. To obtain a serial number for your computer complete this form and email it to

Our flow cytometry experts are available to help analyze data but you can also find videos and tutorials with demo data on the FlowJo website.

Spectral Viewer

Several flow cytometry companies, including BD Biosciences eBioscience and ThermoFisher Scientific, have created fluorochrome spectral viewers to facilitate panel design and have a theoretical prediction of the compensation. These online tools are designed to aid customer understanding of 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. The CRI Flow Cytometry Facility recommends using Fluorofinder to help you in this task.

Setting 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 a new way 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.

A key challenge in flow cytometry is communicating the results along with sufficient experiment details to allow for additional analysis. In Cytobank, users provide these details during the course of analysis, allowing you to start with analyzed or gated data, drill down to the raw data and export gated or raw data in tab-delimited or FCS formats.


Nicolas Loof, M.S.

CRI Research Shared Facilities Manager

Terry Shih, M.S.

Flow Cytometry Specialist