xenium

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

Cross-modal registration of Xenium spatial transcriptomics and MACSima multiplexed immunofluorescence at single-cell resolution.

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 types and tissue structures from H&E across cancers: molecular definition of tumor boundaries, TLS and nerve regions, paired-image alignment, and the H&E models trained on them

A static, highly reactive web browser for spatial transcriptomics and snRNA-seq

A napari-based viewer for Xenium 3.x spatial transcriptomics that records every action as a provenance graph and exports it as a replayable Jupyter notebook.

Cell-resolved Xenium analysis of ion-channel expression and stromal cell states in treated pancreatic ductal adenocarcinoma

Perform Cell Segmentation with a variety of Algorithms on Xenium output.

Scalable mean-field variational HMRF for spatial domain identification at single-cell / million-spot scale

Selective depletion of upper-layer somatostatin interneuron subtypes in schizophrenia: seven-cohort snRNA-seq meta-analysis, Xenium spatial replication, and SCZ common-variant genetics

Xenium literature public-code atlas: 72 repos archived, audited, distilled into an iterable textbook pipeline