Center for Spatial Omics

Data analysis services

Primary processing and pipeline development

•  Automated, high-performance pipelines for image processing, cell segmentation, and molecular quantification across technologies.

Quality control (QC)

• Filtering and normalization, monitoring metrics such as feature counts, UMI distributions, and tissue integrity to ensure data reliability.

Cell-type deconvolution and annotation

• Integration of spatial transcriptomics with single-cell RNA-seq (scRNA-seq) references to resolve cell identities and map their precise locations. This includes both reference-based label transfer and de novo annotation of novel cellular states within the tissue architecture.

Advanced spatial analytics

• Investigation of the "spatial connectome," including cell-cell interaction analysis, neighborhood/niche identification, and spatial trajectory inference.

Multi-omic integration

• Computational strategies to merge transcriptomic, proteomic, and epigenetic layers, providing a unified view of the tissue microenvironment.

Interactive visualization and support

• Delivery of data in user-friendly formats and interactive dashboards, coupled with expert consultation to help investigators interpret complex spatial patterns.
  
   

Available spatial platforms

GeoMx Digital Spatial Profiler (Bruker Spatial Biology)

• Enables highly multiplexed, spatially resolved profiling of RNA (whole transcriptome) and protein (1200 targets) from tissue sections using region-of-interest (ROI) selection. Supports flexible experimental design for discovery and targeted studies and includes custom antibody testing services.

Visium HD (10x Genomics)

• Provides whole-transcriptome sequencing with high spatial resolution on FFPE tissue sections. Ideal for unbiased transcriptomic mapping across tissue architecture and supports custom probe spike-in services to enhance assay flexibility.

CosMx Spatial Molecular Imager (Bruker Spatial Biology)

• Delivers single-cell and subcellular resolution for spatial RNA (up to ~1,000 genes) and high-plex protein detection, enabling true same-cell multiomic analysis. Includes custom RNA probe and antibody design services.

Xenium In Situ (10x Genomics)

• An imaging-based platform for high-plex RNA detection (up to ~5,000 gene targets) with subcellular resolution, with optional integrated protein analysis. Supports custom probe design for targeted and pathway-focused studies.

PhenoCycler Fusion (Akoya Biosciences)

• Designed for highly multiplexed spatial protein imaging, enabling deep phenotyping of tissue architecture and cellular interactions. Includes custom antibody conjugation services for tailored panel development.