Tumor Cartography Core

The Tumor Cartography Core provides essential services to the MGB Cancer Institute and the broader resesarch community, offering investigators access to cutting-edge equipment and expert support for TMA construction, biomarker staining (including multiplex RNA and protein), high-resolution imaging, digital image analysis, and spatial transcriptomics. What sets us apart is our comprehensive, end-to-end approach - guiding projects from sample creation through advanced analysis. Our expertise at every stage of the pipeline ensures high-quality, reproducible data, maximizing the impact of each study.

Key Services:

TMA Construction

Tissue Microarray (TMA) construction is available for formalin fixed paraffin embedded (FFPE) tissue blocks.  We offer a range of geometries compatible with IHC/RNA staining or spatial transcriptomics platforms.

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 is performed on a Leica Bond RX auto-stainer to facilitate high-volume and consistent staining. 

For investigations of 1-2 biomarkers, chromogenic (single-plex 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. We offer a large menu panels that can be used off the shelf or adapted for individual project goals. 

Imagers

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

Zeiss LSM980 Super Resolution 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

Quanterix PhenoImager HT 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)

Image Analysis

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 classification of regions or cells
• Cell phenotyping and enumeration
• RNA ISH quantification
• Spatial profiling
• Heatmap generation
• Tissue registration
• Spatial neighborhood analysis

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 deeper insight using the Bruker GeoMx Digital Spatial Profiler, Bruker CosMx Spatial Molecular Imager, or the 10x Genomics Xenium In Situ platform. These technologies add spatial context to transcriptomic (and, where applicable, proteomic) measurements on a single tissue slide.

• GeoMx (RNA & protein): Quantitative, targeted spatial profiling from user-defined regions of interest (ROIs) within an FFPE tissue section, measuring hundreds of transcripts (including whole-transcriptome workflows) and hundreds of proteins per slide.
• CosMx (RNA & protein): High-plex, single-cell spatial analysis from a single FFPE slide, up to 6,000 genes and up to 68 proteins (panel-dependent).
• Xenium (RNA & protein): Single-cell spatial transcriptomics with panels up to 5,000 genes. Xenium can also be run with 27 protein markers (RNA+protein bundle) and uses rolling amplification chemistry to drive higher signal and sensitivity.

Core support: Our staff can prepare and section FFPE tissue onto platform-specific slides, perform the full spatial workflow (wet lab through instrument run), and provide downstream bioinformatics and data interpretation support.

Publication Acknowledgement

Please cite Mass General Cancer Center Cartography Core in the Acknowledgements section. For more involved projects, co-authorship is requested.  
"We thank the Mass General Brigham Cancer Institute Cartography Core, which provided support for (staining, imaging, image analysis, spatial profiling, insightful discussions...)."
To ensure proper acknowledgment of the resources and funding that support the 10x Genomics Xenium platform, we kindly request that users of the platform include the following statement in their publications or presentations:  "Data generation was made possible by the Cartography Core and NIH S10 equipment funding."