Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
Cell-GPS is the Python package and reference implementation for Cophenetic Spatial Topology Embedding (COSTE), a spatial topology analysis framework for spatial omics data.
Production framework for 10x Visium, Xenium, and MERFISH spatial transcriptomics. Includes Squidpy spatial neighborhood analysis, ligand-receptor cell communication, and WebGL overlays.
Additional MultiQC report sections for 10x Genomics Xenium data.
Python toolkit for image-based spatial transcriptomics (CosMx, MERFISH, Xenium). Unified data object for expression, polygons, and FOV images, plus QC, clustering, point- and polygon-based spatial statistics, and polygon-native cell-cell communication using real membrane contact geometry.
Conservative, reversible transcript-ownership proposals for Xenium spatial transcriptomics.
Cell-resolved Xenium analysis quantifying KCNMA1 spatial organization in fibroblast niches and its association with the PDAC tumor-stroma interface
Cell-resolved Xenium analysis of ion-channel expression and stromal cell states in treated pancreatic ductal adenocarcinoma
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