Histology Spatial Topology for Omics Profiling and Inter-section Alignment
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc.)
Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.
End-to-end analysis of spatial multi-omics data
Interactive visualization of spatial omics data
Single-cell spatial omics analysis that makes you happy!
Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
Spatial analysis toolkit for single cell multiplexed tissue data
conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics
Interoperability between SpatialData and the Xenium Explorer
DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data
A modern Python library for converting Mass Spectrometry Imaging (MSI) data into standardized SpatialData/Zarr format, enabling seamless integration with spatial omics analysis workflows.
Patho-DBiT is a platform to spatially decode RNA Biology in archival FFPE tissues.
OMERO.web plugin for the Vitessce multimodal data viewer.
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).
Companion code for Shulman et al., Cell 2026: AI-predicted spatial transcriptomics unlocks breast cancer biomarkers from pathology.
Quantifying predictability of gene expression from histology image
Quantifying senescence, the easy way.
A standalone, GUI for Mass Spectrometry Imaging (MSI) analysis, combining unsupervised tissue segmentation, spatial molecular profiling, and supervised classification.
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