Ragon Institute Immunology Core-Microscopy

The mission of the Ragon Institute Immunology Core-Microscopy 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 high-throughput and multiplexing slide scanners (TissueFAXS confocal for 120 slides/5 colors and plus for up to 8 slides/10 colors) for rapid imaging of tissues and adhered cell populations, high resolution confocal imaging of multiwell plates or other carriers (Zeiss Celldiscoverer 7 with LSM900 confocal and Airyscan 2 super resolution), and advanced automated live cell imaging applications. There is also high-speed, flow-based imaging of cell populations in suspension using the ImageStreamX Mk II imaging flow cytometer by Cytek. Our facility is unique in that our confocal and live cell imaging capability is situated in a BSL2+ 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@mgh.harvard.edu

Facilities and Equipment:

Visit our flow cytometry page for information about cytometry and cell sorting:

Microscopy (400 Technology Square, Rooms 810 and 812, Cambridge, MA 02139):

  • Zeiss Celldiscoverer 7 with LSM900 confocal and Aiyrscan 2 super resolution (CD7+LSM900) An automated imaging platform especially suited to multi-well plate (up to 1536 wells) imaging in epifluorescence (7 channel LED with CMOS camera), brightfield (various modalities, and laser scanning confocal (in 2D, 3D and 4D) with long-term, time-lapse imaging capability of living or fixed cells and tissues. It also accommodates glass slides, multi-chambered slides (up to 3 slides at a time), and Petri dishes of various sizes. Can also perform high-speed, wide-field epifluorescence in 3D with deconvolution. Airyscan 2 permits rapid super-resolution imaging of 120nm resolution using any fluorophores compatible with the confocal lasers/filter sets (in 2D or 3D). The system is capable of live cell imaging over extended periods (up to days) with built-in temperature and CO2 control. Capable of multispectral imaging (lambda stacks), as well as FRAP, FLIP, and FRET. 
  • TissueFAXS SLQ Spinning Disc, confocal slide scanner by TissueGnostics (TissueFAXS Confocal) Automated and high-throughput (up to 120 slides), high-resolution confocal slide scanning system with the ability to scan entire tissue sections or cultured cell populations on defined regions of slides at 5x, 10x, 20x (typically), 40x, or 63x oil immersion magnification in either brightfield, epifluorescence or confocal modalities (for confocal either single plane or z-stacks, although extended focus is available in brightfield and epifluorescence as well). Previews performed at 2.5x. Equipped for up to 5-color channel fluorescence imaging including DAPI/AF488/AF555/AF647 and AF750. Cell populations can be rapidly quantified with an approach similar to flow cytometry using TissueQuest (fluorescence), HistoQuest (brightfield), or StrataQuest (both with tissue structure quantification) image analysis software. Based on a Zeiss AxioImager Z2 microscope stand.
  • TissueFAXS whole slide scanning system by TissueGnostics (TissueFAXS plus) An automated and high-speed slide scanning system with the ability to rapidly scan entire tissue sections or cultured cell populations on defined regions of slides at 5x, 10x, 20x, 40x, or 100x magnification in either brightfield or epifluorescence (takes up to 8 slides at a time) using a Lumencor Spectra 3, 8 LED light engine (500 mW per channel). Equipped for up to 10-marker/fluorescent channel imaging, as well as iterative, multiple-round multiplexing for even more (unlimited) markers in tissue. Cell populations can be rapidly quantified with an approach similar to flow cytometry using TissueQuest (fluorescence), HistoQuest (brightfield), or StrataQuest (both with tissue structure quantification) image analysis software.
  • Cytek ImagestreamX Mark II (Imagestream) An imaging flow cytometer with two cameras, 12 channels, 405, 488, 561 and 642 nm lasers (along with a 785 nm laser for darkfield SSC). Equipped with 20x, 40x and 60x objectives. Can do extended depth of focus for convolution/deconvolution of images. Usually load 30ul per sample at a time. Capable of capturing up to 60,000 images per second (with binning). Use with IDEAS analysis software. 
  • Image Analysis Workstations Two workstations, one (Image Analysis PC1) equipped with Imaris 2D/3D/4D analysis software (Oxford Instruments), along with the Zen image processing/analysis software for the Zeiss Celldiscoverer 7. There is also a temporary license for Arivis high-end analysis software (part of the Zeiss/Zen bundle). ImageJ, CellProfiler. Image Analysis PC2 has software devoted to the two TissueFAXS slide scanners, namely TissueQuest (for profiling fluorescent cell populations in tissues similar to flow cytometry) and HistoQuest (for profiling cells in brightfield IHC images/tissues). These rely on cell nuclei for quantification. There is also StrataQuest which is higher level analysis software that also deals with tissue structure/cell density/gradients/cell relationships in both fluorescence and brightfield. TissueFAXS Viewer software is also provided. 


  • Consultation in terms of experimental design, fluorophore selection, and the imaging system best suited to the needs of the investigator is provided.
  • Individual training in the use of any of the imaging systems in the core is provided so that users are able to work independently with the systems.
  • For more sophisticated applications, assisted use of the systems is provided.
  • Imaging core staff are available to answer questions or to assist in troubleshooting.
  • Training in image analysis applications is also provided for core users.
  • The core continues to evolve to suit the needs of the Ragon Institute and the greater MGH community. 
We provide training in the use of flow cytometers and assistance in the development of panels and experiment design, as well as access to advanced flow cytometry equipment. Our training program consists of an Introduction to Flow Cytometry seminar offered every 6 weeks, an instrument orientation, and then hands-on training in the proper operation of the equipment. Visit our website linked below for more information.

Getting started:

To access the Imaging Core please email Michael and Thomas 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: