Mass General Krantz Family Center for Cancer Research Cartography Core

The aim of the Imaging Core is to provide comprehensive services for state-of-the-art staining, imaging, and digital image analysis to Cancer Center researchers. The core specializes in high-volume samples, multiplex staining, and spatial image analysis. To learn more about the core please contact the core director to schedule a consultation.

Biomarker Staining

The core offers staining services for FFPE tissue, TMAs, cytology specimens, and cell blocks using the latest chromogenic and fluorescence labels.  All staining, with the exception of DNA fusion, is performed on a Leica Bond RX autostainer to facilitate high-volume consistent stains. 

For investigations of 1-2 biomarkers, chromogenic (singleplex or duplex) stains are recommended. Proteins can be targeted using standard IHC, while high expression RNAs can be visualized using ACD RNAscope probes.

For investigations requiring multiple biomarkers and/or their spatial relationships, multiplex fluorescence panels are recommended. Off-the-shelf multiplex fluorescence (using Akoya’s Automated Lung/Melanoma kit) and CCR developed panels are available for protein and RNA (RNAscope ISH) stains. 


Imagers are operated by trained core staff, except where indicated below.  

Zeiss LSM980 (Airyscan 2) Laser Scanning Confocal*

Laser scanning confocal microscope capable of capturing high resolution images with z-stacks on fixed or live samples.  Second generation Airyscan detection is a method to capture super-resolution images using low light levels.  

  • Multi-position imaging
  • Time-lapse imaging
  • Live cell imaging with incubation and CO2
  • AI sample finder
  • Definite Fous

*Trained users have 24/7 scheduled access to imagers.  Assisted imaging is available upon request for an additional fee.

Zeiss Arivis 3D Image Analysis Platform

Advanced scientific image analysis platform for 3D images.  Capable of AI-driven image analysis, tile stitching, 4D tracking and lineage, segmentation, batch analysis pipelines, and more.

MoticEasyScan Infinity Digital Pathology Scanner

Automated whole slide pathology scanner ideal for IHC, H&E, or RNA-ISH chromogenic stains.

  • Choose from dry scanning 20x or 40x
  • Z-stacking and extended depth of field (EDF) capability
  • Superb image quality for publication or downstream image quantification
  • Ideal for IHC FFPE tissue sections or hematology and cytology slides

Akoya Polaris Slide Scanner 

Automated multispectral fluorescence slide scanner capable of 20x and 40x resolution images as well as bright field imaging and  standard fluorescence scans.  Ideal for:

  • Multiplexed fluorescence IHC or RNA ISH stains
  • Samples with high confounding autofluorescence (like FFPE specimens)

Akoya Vectra Slide Scanner 

Multispectral fluorescence slide scanner capable of 10x and 20x resolution images.  

Image Quantification

Digital image analysis can be performed by core staff using high-end software (Halo AI by Indica Labs or VIS by Visiopharm) for a range of applications  including:

  • AI segmentation of regions or cells
  • Cell phenotyping and enumeration
  • RNA ISH quantification
  • Spatial profiling
  • Heatmap generation
  • Tissue registration

Each customized analysis app produces a summary table containing the total number of cells, tissue area, cell phenotype numbers and percentages, mean staining intensity for each cell phenotype, and more. Individual cell information (i.e. object data tables) can also be exported, containing information such as individual cell staining intensity, cell size, and XY cartesian coordinates for more complex analyses using custom R or Python scripts. 

Spatial Transcriptomics

Explore spatial biology with greater insight using Nanostring GeoMx Digital Spatial Profiler or Nanostring CosMx Spatial Molecular Imager. These platforms provides spatial context to transcriptomic and proteomic experiments within a single slide.  GeoMx RNA and protein assays enable quantitative and targeted spatial profiling of 100s of transcripts (up to the whole transcriptome) and 100s of proteins from a select regions within a single FFPE tissue section.  CosMx RNA assays enable high-plex single-cell analysis of up to 6,000 genes and 68 proteins from a single FFPE slide.


Please cite Mass General Cancer Center Translational Cartography Core in the Acknowledgements section. For more involved projects, co-authorship is requested.  

"We thank the Mass General Cancer Center Translational Cartography Core, which provided support for (staining, imaging, image analysis, spatial profiling, insightful discussions...)."


For scheduling initial consultation meeting, please contact Danielle Bestoso, program manager, at

For training requests, please contact Katherine Xu at