MGH Cancer Center/Molecular Pathology Confocal Core

In order to ensure the safety of all users, we require that:

1.  MGH-provided surgical masks are required at all times

2.  Users wipe down surfaces before *and* after use.  70% ethanol and kimwipes will be provided.  

As a reminder, high touch surfaces include: mouse, focusing knobs, keyboard, etc.  

Please use lens paper to clean eye pieces.  

If you have any questions or concerns, feel free to contact Linda Nieman at

Thank you for your cooperation.


The MGH Cancer Center and Molecular Pathology Core is a limited core available to Cancer Center and Molecular Pathology members only.  Trained users have 24/7 scheduled access to our Zeiss LSM710 inverted confocal microscope. All training is free of charge, but requires refresher training session if one hasn’t used the system for six months or more.

Key features:

    - Laser scanning confocal microscope for acquiring high resolution images

    - Fixed or live samples using 6 different laser excitation lines (405, 458, 488, 514, 561, 633 nm)

    - Multi-position imaging

    - Time-lapse imaging

    - Live cell imaging with CO2 and incubation

Image analysis can be performed using Zeiss Zen software or Zen Lite (available for free download)

The LSM710 is located on 7th floor of CNY149.

Publications:  Please cite MGH Cancer Center / Molecular Pathology Confocal Core in the Acknowledgements section.

Please submit training or assisted imaging requests to Linda Nieman at and Katherine Xu at

Message to the Core

Confocal Specifications

Confocal Manual

Fee Structure

Additional systems available for use after consultation with Dr. Nieman:

Leica Aperio CSO Digital Pathology Scanner

Automated pathology microscope scanner ideal for scanning IHC tissue slides, with capability of scanning up to 5 slides in a single set up.

  • Choose from dry scanning 20x or 40x
  • Superb image quality for publication or downstream image quantification
  • Ideal for IHC FFPE tissue sections or hematology and cytology slides

Nikon 90i Upright Research Microscope

High quality research microscope perfect optimized for digital imaging.  Unique “fly-eye” optics and VC-series objectives enable the ECLIPSE 90i to capture images with excellent resolution and uniform brightness up to the edges.  With low noise fluorescence imaging capability and DIC flexibility, it is perfect for capturing publication quality images quickly.

  • Choose from a range of dry (4x, 10x, 20x, 40x, 60x) and immersion objectives (40x, 100x)
  • Capable of fluorescence and brightfield modes
  • Long working distance objectives allow visualization of non-standard samples such as microfluidic chips
  • Superb image quality for publication or downstream image quantification

Perkin Elmer Vectra3 Multispectral Slide Scanning Microscope

Vectra3 multispectral imaging system, together with the inForm® software, provides mutlsipectral and automated multi-slide imaging of up to 6 slides to detect and measure weakly expressed and overlapping biomarkers in H&E, IHC, or IF intact FFPE tissue sections of TMAs

Tissue sections or TMAs can be labeled with immunofluorescent (IF) or immunohistochemical (IHC) stains such as Opal, or with conventional stains such as H&E and trichrome. When using IF or IHC stains, multiple proteins can be measured on a per tissue, per cell, or per cell compartment (e.g. nuclear, cytoplasmic) basis - even when signals are spectrally similar, are located in the same cellular compartment or are obscured by autofluorescence.

  • Supports PerkinElmer’s Phenoptics workflow solution for cancer immunology research
  • Detects and measures multiple weakly expressed and overlapping biomarkers within a single H&E, IHC or IF tissue section and in TMAs
  • Visualizes, analyzes, quantifies and phenotypes immune cells in situ in solid tissues
  • Automatic identification of specific tissue types using integrated inForm analysis software

Visiopharm Quantitative Digital Image Analysis Software

Advanced digital image analysis software for quantification using high-level and intuitive language to define custom image analysis APPs.

  • Infinitely configurable and does not require programming skills (but it is helpful)
  • Develop and design apps for automated batch analysis of images
  • Permits highly sensitive, reliable, and reproducible automated quantitative biomarker assessments compared to manual reading

Halo Quantitative Tissue Analysis Software

Image analysis platform that is intuitive and scalable, with powerful and fast analytic capabilities. 

  • Reports morphological and multiplex expression data on a cell-by-cell basis across entire tissue sections while maintaining an interactive link between cell data and cell image
  • Sorting and filtering capabilities allow user to mine millions of cells while visually assessing corresponding cell populations
  • Data is exportable for in-depth analysis in R, Python, or other data analysis software