Models & Data

Foundation model for spatial proteomics. Code and weights are available for academic research.

A Foundation Model for Spatial Proteomics arXiv, 2025

Code and weights for KRONOSHugging Face for KRONOS

Self-supervised cell representations from expression, neighborhood and image.

CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data Nature Immunology, 2025

Code for CellLENSCODEX tonsil data for CellLENS

Cell type annotation from spatial proteomics.

MAPS: pathologist-level cell type annotation from tissue images through machine learning Nature Communications, 2024

Code for MAPSData for MAPS

Single-cell matching and integration across modalities.

Robust single-cell matching and multimodal analysis using shared and distinct features Nature Methods, 2023

Code for MARIO

Spillover correction for multiplexed images.

Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images Frontiers in Immunology, 2021

Code for REDSEA

Plotting code and a template for automating PASTA on the Opentrons OT-2.

PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology Nature Methods, 2026

Code for PASTAImages and data for PASTA

Analysis code and SGCC tutorials, with protocols and videos for each platform combination.

Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment Cancer Discovery, 2026

Code for IN-DEPTHProtocols and videos for IN-DEPTHSGCC on CRAN for IN-DEPTHData, first release for IN-DEPTHData, second release for IN-DEPTH

Probe design for 16S rRNA imaging and the full analysis.

A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment Nature Communications, 2025

Probe design for MicroCartAnalysis code for MicroCartData for MicroCart

Code that goes with our MIBI workflow chapter.

A Hitchhiker’s guide to high-dimensional tissue imaging with multiplexed ion beam imaging Methods in Cell Biology, 2024

Code for MIBI guide

Analysis code, and the MIBI and imaging mass cytometry images from the paper.

Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology Nature Communications, 2023

Code for ExPRESSOMIBI data for ExPRESSO

Analysis code, with the multiplexed images on the MIBItracker.

Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments Immunity, 2022

Code for PANINICode archive for PANINIImages on MIBItracker for PANINI

Code and RNA-seq data for high-definition ion beam imaging of biomolecules and drugs inside cells.

Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging Nature Communications, 2021

Code for HD-MIBIRNA-seq data for HD-MIBI

MIBI images and the code behind every figure.

Spatial Proteomics Uncovers Immune Cell Neighborhoods and Tumor-Immune Interfaces in Pancreatic Ductal Adenocarcinoma Molecular & Cellular Proteomics, 2026

Code for Pancreatic cancerMIBI data for Pancreatic cancer

CODEX images and code, with single-cell, GeoMx, Visium HD and bulk RNA data. Raw sequencing data are under controlled access.

Follicular Lymphoma Transformation is Characterized by Cytokine-associated Remodeling of Stromal and Macrophage Compartments Cancer Discovery, 2026

Code for Follicular lymphoma transformationCODEX data and code for Follicular lymphoma transformationscRNA-seq data for Follicular lymphoma transformationGeoMx data for Follicular lymphoma transformationVisium HD data for Follicular lymphoma transformationBulk RNA-seq data for Follicular lymphoma transformationRaw sequencing data (dbGaP) for Follicular lymphoma transformation

GeoMx counts, CODEX images and single-cell CODEX data, with the analysis code.

Coordinated immune-epithelial dynamics in the nasal epithelium protect against respiratory virus infection bioRxiv, 2026

Code for Nasal immune-epithelial dynamicsData for Nasal immune-epithelial dynamics

Images, segmentation masks, Seurat objects and analysis code.

Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment Cell Reports Medicine, 2026

Code for EBV in Hodgkin lymphomaCode archive for EBV in Hodgkin lymphomaData for EBV in Hodgkin lymphoma

Raw reads from the genome-wide CRISPR screen that found desmocollin 2.

Epstein-Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor Nature Microbiology, 2025

CRISPR screen data for EBV entry receptor

Spatial profiling data and code, and a portal to browse the single-cell and spatial data.

Multi-scaled Transcriptomics of Chronically Inflamed Nasal Epithelium reveals Immune-Epithelial Dynamics and Tissue Remodeling in Nasal Polyp Formation Immunity, 2025

Data and code for Chronic rhinosinusitisData portal for Chronic rhinosinusitis

HiChIP, Hi-C, 4C-seq, CUT&RUN and ChIP-seq data.

A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth Nature Communications, 2023

Sequencing data for EBV and the host 3D genome

Code to measure membrane ACE2 in tissue images.

Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers Cell Reports Medicine, 2021

Code for SARS-CoV-2 entry in the airway