Useful Info in Flow Cytometry



Main Duke Medical Center Campus
  • Cell Analyzers:
    • Fortessa (F01) - RP, Room 105
    • iQue (Q01) - MSRBII, Room 4036
    • LSR II (L01) - RP, Room 105
    • LSR II (L02) - RP, Room 105
    • Muse (M01) - RP, Room 105
  • Cell Sorters:
    • Aria II (A01) - GHRB, Room 1071 (normal or high-containment; RBL at Duke)
    • Aria II (A02) - MSRBII, Room 4036
RTP Duke Campus
  • Cell Analyzers:
    • Muse (M02) - RTP, Room 2104
    • Symphony A5 (P01) - RTP, Room 2104B
    • BD Rhapsody (R01) - RTP, Room 2104C
  • Cell Sorters:
    • Symphony S6 (S01) - RTP, Room 2104D


  • Always carry your Duke ID for access

  • Contact Facility Director for DukeCard access to any of these buildings


  • The Duke Human Vaccine Institute Flow Facility is capable of performing analysis and sorting of fixed and unfixed specimens from a wide-range of sources. 

  • We have the capability to safely work under Biosafety Levels 1, 2 and 3 and are registered to work with Select Agents.

  • A Hazard Assessment review of new projects will dictate the appropriate SOP for us to follow. This process is initiated BY THE END USER by completion of a simple online form.  

  • In conjunction with the DHVI Safety Team, the leadership of the RBL at Duke and the Duke Occupational and Environmental Saftey Office (OESO), we have developed Standard Operating Procedures for our facility.  These documents dictate how we work with your specimens in our facility.  

  • For PIs/End Users that need to provide protocol and procedure documentation to the Duke IBC, these documents can be attached to their registration and indicate that work will be performed in the DHVI Research Flow Cytometry Facility.

Data Management:

Protocol/Procedure Share Library:

Please email a PDF copy of a protocol you would like to share on this web page to user support  (Please include your name and the name of the submitting lab)

 Mouse Tissue/Cell Isolation:

Mouse Sample Staining/Preparation:

Human/Non-Human Primate Tissue/Cell Isolation:

  • Coming Soon!

Human/Non-Human Primate Sample Staining/Preparation:

  • Coming Soon!

Misc. / Other:

DISCLAIMER:  The DHVI Flow Facility has not specifically tested all of these protocols and make them available with no gaurantee. Contact the submitting end user or Lab PI as indicated in the File Name. 

Please acknowledge the Duke Human Vaccine Institute Flow Facility in your publications:

“Flow cytometry was performed in the Duke Human Vaccine Institute Flow Cytometry Facility (Durham, NC).”

For work conducted on the A01, please add the following sentence to your acknowledgments:

"Flow cytometry was performed in the Immunology Unit of the Regional Biocontainment Laboratory at Duke, which received partial support for construction from the National Institutes of Health, National Institute of Allergy and Infectious Diseases (UC6-AI058607)"

Email us a PDF of your paper acknowledging the DHVI Flow Facility to earn a free hour of flow time! 

Panel Design

Online Tools:

  • FluoroFinder

    • Fluorofinder is a free flow cytometry resource to streamline design of panels on your favorite DHVI cytometer: 
    • Fluorofinder helps eliminate challenges and headaches associated with designing flow cytometry panels/experiments for our specific instruments. 
    • Highlights include:
      • Antibody Search Tool – Real time feedback on over 145,000 reagents and 354 fluorochromes available on the cloud-based tool
      • Customizable – Multicolor panels that work with DHVI cytometer configurations
      • Free - Individual accounts at no cost to academic/nonprofit institutions & researchers
    • For a quick walk through the panel building process, watch this YouTube video.
  • BD HorizonTM Guided Panel Solution (GPS)

    • ​GPS provides a guided workflow for reagent selection based on the principles of panel design.
    • Use is free but users must create an account. Panels can be saved. 

Instructional Resources:

  • Principles of Panel Design: a PDF from BD showing key concepts for the design of multicolor flow cytometry panels
  • Spectrum Viewer: a helpful tool from BD to determine optimal laser and filter combinations for different fluorochromes.

Data Analysis

Online Tools:

  • FlowJo

    • FlowJo® is the leading analysis platform for single-cell flow and mass cytometry analysis
    • Individual licenses can be obtained through the DHVI flow facility (link).
  • Cytobank

    • Cytobank is a cloud-based platform specializing in the analysis and visualization of multiple single-cell data sets simultaneously.
    • Tools include SPADE, viSNE, and CITRUS analyses.
    • Monthly fee; free 30-day trial.

    • SPICE is a data mining software application that analyzes large FlowJo® data sets from polychromatic flow cytometry and organizes the normalized data graphically.

Introduction to Flow Cytometry (Required Online Course)

  • Take the quizzes at the end of each section
  • Record quiz results and bring to Classroom Session

DiVa Training Manual

  • Focus on: The BD FACSDiva Workspace, Cytometer Acquisition Controls, Tools for Data Analysis (Chapters 2-4)



Q. I’m a new user. How do I schedule time with the DHVI Flow Facility?

A. Visit our "Get Started" page for details on using the DHVI Flow Facility.

Q. Can a Flow Facility Operator run my phenotyping samples?

A. No, we are no longer offering operator-assisted phenotyping. Contact the DHVI Flow Facility Director at (919) 681-8193 for special requests/collaborations

Q. How do I get trained to use the cytometers?

A. Follow the "Easy Steps to Using the DHVI Flow Facility." Please note you will need to be linked to your PI and a fund code in CoreResearch.

Q. How do I get linked to a project (fund code) and/or PI in CoreResearch?

A. New users can be linked to projects and PIs by a PI, PI-delegate, or financial administrator. Please contact the appropriate personnel in your lab or department and indicate that you need to be linked to a project and PI in CoreResearch. You will need to be linked to a project and PI in order to make reservations on CoreResearch. 

Q. How do I register for a FlowJo site license or change my current hardware address?

A. Submit a request. Please note you will need to be linked to a valid fund code in CoreResearch.

Q. How do I retrieve my flow data from the flow facility?

A. If you are using the analysis cytometers as an independent user, you will transfer your data from the facility computers to your computer using your Duke Box account. If you used the facility for sorting, you will receive an email link from the facility to retrieve your data files.

Q. How can I know which cytometer is best for my panel of reagents (fluors)?

A. See Instrument Configurations in Download Library. Or, visit Fluorofinder to build antibody panels customized for our instruments.

Q. I am new to immunophenotyping and flow cytometry.  How do I prepare samples for flow analysis?

A. For sample preparation, see our Protocols/Procedures.  For customized consultation on assay and panel design contact the Facility Director.

Q. I've signed up to sort on the A01, but how do I get to the GHRB building?

A. The GHRB building is located behind MSRBII - from Research Drive, walk past MSRBII then go down the steps to the right. At the gate intercom, call security for access. Once inside GHRB, you will pass through an airport-like security check. Security will call your operator, who will then meet you in the lobby and escort you to the A01.