Flow Cytometry and Microscopy Services

Immunology Core confocal microscope images

The Immunology Core provides the Harvard University AIDS research community access to and training in leading-edge technology, techniques and assays addressing questions relevant to immunology and infectious diseases. The core consists of two sites:

  • The Center for Virology and Vaccine Research (Site A; BIDMC) assists investigators with questions pertaining to the immune control of HIV, nonhuman primate immunodeficiency viruses, as well as other viruses that impact immuno-suppressed individuals.Sorting capabilities include the ability to sort live, infectious cells in a biosafety cabinet in a BSL2+ laboratory. 
  • The Ragon Institute of MGH, MIT and Harvard (Site B; MGH) is located at 400 Technology Square in Cambridge and provides unparalleled access and service for a broad range of flow cytometry, cell sorting, and protein analysis applications, as well as advanced microscopy, live cell imaging, and image analysis applications.


Flow Cytometry

  • Flow Cytometry. Five different analysis flow cytometers equipped with two to five lasers and capable of measuring up to 18 colors. At BIDMC, there are 2 flow cytometers equipped with 4 lasers that are capable of measuring up to 18 colors and one cell sorter with 4 lasers, capable of measuring up to 18 colors and sorting up to 8 populations.
  • Cell Sorting. A five laser, 21 parameter sorter can sort up to six different populations at a time, and is housed in biosafety level 2+ (BL2+). 
  • Mass Spectrometry. A DVS Sciences CyTOF mass cytometer is available for detecting over 30 parameters at a time.
  • Imaging Cytometry. An ImageStreamX Mark II imaging cytometer by Amnis combines the high-data content of microscopy with the high throughput of flow cytometry, and is equipped with 4 different laser lines to capture images of cells in up to 12-channels at different magnifications (20x, 40x, 60x).
  • Protein Interactions/Kinetics. Label-free protein interactions and binding kinetics can be detected using a Biacore 3000 through SPR (Surface Plasmon Resonance).
  • Luminex technology allows users to measure the presence of multiple proteins or other molecules in a sample, as well as permitting measurement of up to 500 different analytes in a single sample.
  • Training. Provide SOPs and formal needed training in use of core equipment and related techniques. Provide classes in flow cytometry and flow cytometry applications.

For more information on the Ragon Institute Flow Cytometry division, please refer to the website: http://www.ragoninstitute.org/research/services/flow-cytometry/


  • Zeiss LSM510 laser scanning confocal inverted microscope. Four lasers, seven excitation wavelengths, four reflected light path PMTs and one transmitted light path PMT. Fixed and live cell confocal imaging, time-lapse live cell imaging (temperature and CO2 control), multiple positions over time, 3D reconstruction, FRET, FRAP.
  • Zeiss Axio Observer Z1 Automated Microscope.  Automated multi-channel epifluorescence imaging system for time-lapse live cell imaging capability (temperature and CO2 control), high-throughput multi-well plate imaging, high-speed live cell imaging, ratiometric imaging, and 3D image stack capture with piezo focus for deconvolution.
  • Zeiss Axio Observer A1 manual fluorescence microscope. Equipped with a 12 bit AxioCam MRc color CCD camera and Axiovision image capture software from Zeiss.
  • TissueFAXS Whole Slide Scanning System. An automated and rapid slide scanning system for scanning cells or tissues over entire slides or regions of slides at 10x, 20x, 40x, or 100x magnification, in either brightfield or epifluorescence. Cell populations with multiple labels can be rapidly quantified using TissueQuest or Histoquest image analysis software.
  • Zeiss MIRAX MIDI Slide Scanner. Computer controlled, automated slide imager (up to twelve slides per run) for either brightfield or fluorescence imaging. Creates stitched composites of entire slides as a single image using Zeiss software for analysis.
  • Image Analysis. Training and access to advanced image analysis software, including Imaris Image Analysis Software Suite with Imaris Batch (Bitplane) for 2D/3D/4D analysis, Metamorph Image Analysis Software (Molecular Devices), TissueQuest and HistoQuest cell population analysis software (TissueGnostics)
  • Training and Education. Provide formal needed training in use of microscopy equipment and related techniques. Training and consultation provided in advanced image analysis techniques and applications. Training course provided in introductory microscopy, imaging applications and analysis. SOPs relevant for equipment use also provided. 

For more information on the Ragon Institute Microscopy division, please refer to the website: http://www.ragoninstitute.org/research/services/microscopy/

Training and Education Links         

Flow Cytometry Division 

Investigator Sort Form PDF (BIDMC)   

LSR II and LSR Fortessa User Guide
Calibur User Guide
Intro to Flow presentation
Tracking settings with beads
Sorting Guidelines
Sort Request Form Instructions
Sort Request Form

Microscopy Division

Ragon Core User agreement 2013
Ragon Imaging Core SOP 2013
BL2 Confocal access form
Microscopy Policies