scAtria single-cell spatial atlas resource

single-cell Atlas of Tissue Regional and Interactive Architecture

A curated atlas for exploring single-cell spatial datasets across tissues, regions, and cellular interactions.

Examples Study ID HNSCC_41616773 Organ breast Title lymph node colonization PMID 41616773 Technique Xenium
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Datasets
94
Browse
Samples
7,709
Browse
Studies
82
Study summary
Cells
128,508,915
Spatial transcriptomics (ST)
61 datasets 1,777 samples
Browse
Spatial proteomics (SP)
33 datasets 5,932 samples
Browse
Technique Map

What spatial techniques have we covered?

Click a bubble to browse that technique.

Anatomy Map

Which organs do the datasets profile?

Click an organ to review datasets and samples.

Anatomy Detail

Lung

Browse by dataset Browse by sample
Datasets
13
Samples
2,814
Studies
13
Curated
11
Cells
15,259,149
Dataset Technique Samples Cells Curation
10x Genomics Visium HD p2 TissueArray showcase Visium HD 1 113,248 Curated
10x Genomics Visium HD showcase Visium HD 5 914,818 Curated
10x Genomics Xenium Prime 5K showcase Xenium 1 278,328 Curated
LUAD_36725934 � IMC 416 1,635,722 Curated
MERFISH 500-plex Vizgen showcase MERFISH 2 1,190,501 Curated
NSCLC_38242124 � IMC 2,070 5,984,454 Curated
NSCLC_40408481 � PCF 257 1,450,507 Curated
PulmonaryFibrosis_39901013 � Xenium 45 790,934 Curated
Xenium Human Immuno-Oncology Profiling Panel showcase Xenium 1 161,000 Curated
Xenium Human Lung Gene Expression Panel showcase Xenium 3 1,105,707 Curated
Xenium Human Multi-Tissue and Cancer Panel showcase Xenium 2 312,619 Curated
DevelopingLung_39477961 � PCF 5 971,112 Source
NSCLC_40220761 � CosMx SMI 6 350,199 Source
Cell Ontology Map

How cell ontologies connect across tiers

Hover on a node to trace its lineage.

117,717,280 curated cells 192 ontology paths
Tier 1 Tier 2 Tier 3 Tier 4
Spatial Modules

Sample-level architecture, ready to compare

Three precomputed modules summarize domains, cell-type contacts, and graph topology from curated labels and coordinates.

01

Domains

Neighborhood/domain composition by Tier 2 and Tier 3 labels.

 02

Interaction Propensity

Directed Tier 3 and Tier 4 cell-type contact enrichment.

 03

Network Topology

Delaunay graph summaries across Tier 1 through Tier 4 labels.
Open spatial overview Browse curated datasets