Ragon Institute Immunology Core-Flow Cytometry

The mission of the Ragon Institute Immunology Core is to bring the latest imaging modalities to bear on fundamental molecular and cell biological questions pertaining to human disease. As an MGH core facility, it serves the greater MGH community in all aspects of flow cytometry, cell sorting, advanced microscopy and image analysis. The Microscopy division of the Ragon Institute Imaging Core is located on the 8th floor of 400 Technology Square in Cambridge (Main Street). The core offers training, assistance and access to a wide variety of imaging systems including slide scanners (TissueFAXS and Zeiss MIRAX MIDI) for rapid imaging of tissues and adhered cell populations, high resolution confocal imaging (Zeiss LSM510), and advanced live cell imaging systems. There is also high-speed, flow-based imaging of cell populations in suspension using the ImageStreamX MkII by Amnis. Our facility is unique in that our confocal and live cell imaging systems are situated in a BL2S facility. In addition, consultation is provided on sample preparation, experimental design, and advanced image analysis, in addition to assistance with all aspects of the imaging process.

Personnel/Contact Information:

Director: Michael Waring
Email: mwaring@partners.org

Associate Director (Microscopy): Thomas Diefenbach, Ph.D.
Phone: (857) 268-7046
Email: tdiefenbach@partners.org

Facilities and Equipment:

Flow Cytometers (400 Technology Square, room 910 and 911, Cambridge MA 02139):

  • Two 5 Laser LSR Fortessas (BD Biosciences) with 355, 405, 488, 561, and 640 excitation lines, up to 18 colors, and the HTS option for acquiring from 96 well plates.
  • 4 Laser LSR2 (BD Biosciences) with 355, 405, 488, and 633 excitation lines, 16 colors.
  • 3 Laser LSR2 (BD Biosciences) with 405, 488, and 633 excitation, 16 colors, and the HTS option for acquiring from 96 well plates.
  • Imagestream X Mark II (Amnis) imaging cytometer,
  • 5 laser FACSAria cell sorter (BD Biosciences) with 350, 405, 488, 561 and 633 excitation, 18 colors, housed within a biosafety cabinet for sorting of human and infectious samples requiring up to BL2+ containment. The sorter is run by core personnel only, and no training is provided in its operation.
  • 4 laser FACSAria Fusion cell sorter (BD Biosciences) with 405, 488, 561, and 640 excitation, housed in a biosafety cabinet for BL2+ sorting.
  • 4 laser SONY SH800 cell sorter (Sony Biotech) with 405, 488, 561, and 640 excitation and 6 colors.

Additional Equipment:

  • BioPlex 3D (BioRad) and Flexmap 3D (Luminex) XMap readers
  • Computer workstations for data analysis and access to platform-specific software.
Visit our microscopy page for imaging: https://researchcores.partners.org/ragon2/about


  • New users are required to attend our introduction to flow cytometry, "Just the FACS", as well as an instrument orientation session.
  • Consultation in terms of the imaging system best suited to the needs of the investigator is provided.
  • Individual training in the use of the analyzers in the core is provided so that users are able to work independently with the systems.
  • Assisted use of the systems is provided until user is proficient, and all sorting is run by core personnel.
  • The core continues to evolve to suit the needs of the Ragon Institute and the greater MGH community. 

Getting started:

To access our flow cytometry and sorting resources, please email Michael with a description of what resources you were interested in utilizing.

Departmental Web Links:

Ragon Institute Core Services home page: https://www.ragoninstitute.org/resources/cores/

Departmental link: