Spatial transcriptomics
61 datasets · 1,777 samples
About scAtria
scAtria curates 94 datasets from 82 studies, covering 7,709 samples and 128,508,915 cells across 14 spatial transcriptomic and proteomic technologies. Of these, 80 datasets, 7,487 samples, and 118,589,227 cells have curated tiered cell ontology suitable for cross-study comparison.
Each record links study metadata, sample-level organ identity, disease status, cell-ontology tiers, coordinate-linked in situ views, and available spatial or marker outputs. Start from Home, filter records in Browse, inspect study-level dataset pages, review catalog statistics below, explore Domains, Interaction, and Topology, or retrieve tables from Download.
Current published spatial outputs span 71 datasets, 7,269 sample graphs, 1,273,706 interaction pairs, 216,895 topology nodes, 989,821 topology edges, and 79,830 domain entries, supporting cross-organ and cross-condition comparison of spatial compartments, contact structure, and tissue architecture.
Inspired by Roman atria, architectural spaces where light, air, water, movement, and reception came together, scAtria treats cells like inhabitants of a shared tissue interior: spatial context reveals encounters, neighborhoods, and biological exchange.
Catalog and ontology statistics
94
80 curated datasets
7,709
7,487 curated samples
128,508,915
118,589,227 curated cells
272
curated ontology labels
Spatial proteomics
33 datasets · 5,932 samples
Statistics by study
Top studies by cells82 studies
| Study | Datasets | Samples | Cells |
|---|---|---|---|
| MERFISH 500-plex Vizgen showcase | 1 | 18 | 10,196,835 |
| NSCLC_38242124 | 1 | 2,070 | 5,984,454 |
| B-NHL_38379051 | 1 | 35 | 5,690,284 |
| 10x Genomics Visium HD showcase | 1 | 24 | 5,379,712 |
| Xenium Human Multi-Tissue and Cancer Panel showcase | 1 | 20 | 5,095,938 |
| SPATCH_41107232 | 4 | 18 | 4,948,582 |
| 10x Genomics Xenium Prime 5K showcase | 1 | 9 | 4,598,042 |
| DKD_42056516 | 2 | 64 | 4,337,862 |
Statistics by technique
Platform footprint14 technologies
Statistics by anatomy
Organ footprint10 shown
Statistics by cell ontology
Tier summaries272 labels
| Tier 1 label | Cells | Datasets | Studies |
|---|---|---|---|
| Immune | 40,692,308 | 77 | 66 |
| Tumor/Malignant | 30,818,752 | 51 | 47 |
| Stromal | 24,107,754 | 78 | 67 |
| Epithelial | 15,091,372 | 41 | 36 |
| Other | 3,479,430 | 42 | 39 |
| Neural/Glial | 2,225,441 | 21 | 18 |
| Hematopoietic | 1,302,223 | 9 | 8 |
| Tier 2 label | Cells | Datasets | Studies |
|---|---|---|---|
| Tumor/Malignant | 30,818,752 | 51 | 47 |
| Lymphoid | 26,640,949 | 73 | 63 |
| Epithelial | 15,091,372 | 41 | 36 |
| Stromal | 14,600,779 | 69 | 62 |
| Myeloid | 12,667,969 | 73 | 63 |
| Vascular stromal | 9,377,092 | 73 | 63 |
| Other | 3,479,430 | 42 | 39 |
| Neural/Glial | 2,218,239 | 21 | 18 |
| Immune | 1,383,390 | 15 | 14 |
| Erythroid | 1,078,806 | 7 | 7 |
| Hematopoietic progenitor | 199,693 | 3 | 3 |
| Immune-associated stromal | 96,170 | 5 | 5 |
| Skeletal stromal | 28,867 | 3 | 3 |
| Megakaryocytic | 17,430 | 5 | 4 |
| Tier 3 label | Cells | Datasets | Studies |
|---|---|---|---|
| Tumor/Malignant cell | 30,818,752 | 51 | 47 |
| T cell | 14,157,555 | 71 | 62 |
| Fibroblast | 10,719,947 | 56 | 49 |
| B cell | 9,159,236 | 64 | 56 |
| Macrophage | 6,156,901 | 64 | 56 |
| Endothelial cell | 5,344,234 | 73 | 63 |
| Mural cell | 4,032,858 | 39 | 36 |
| Epithelial cell, unspecified | 3,935,409 | 23 | 20 |
| Stromal cell, unspecified | 3,696,984 | 24 | 24 |
| Other | 3,415,470 | 41 | 38 |
| Tubular epithelial cell | 3,196,347 | 5 | 4 |
| Enterocyte | 2,160,453 | 9 | 8 |
| Plasma cell | 1,956,982 | 43 | 41 |
| Myeloid cell, unspecified | 1,736,266 | 14 | 14 |
| Tier 4 label | Cells | Datasets | Studies |
|---|---|---|---|
| Tumor/Malignant cell | 30,818,752 | 51 | 47 |
| B cell | 9,024,583 | 64 | 56 |
| Fibroblast | 9,004,274 | 56 | 49 |
| Macrophage | 6,149,500 | 64 | 56 |
| CD4 Tconv | 5,595,250 | 42 | 34 |
| Endothelial cell | 4,050,020 | 72 | 62 |
| Pericyte/Smooth muscle | 3,964,135 | 37 | 34 |
| Epithelial cell, unspecified | 3,777,697 | 17 | 14 |
| Stromal cell, unspecified | 3,661,788 | 23 | 23 |
| Other | 3,415,470 | 41 | 38 |
| CD8 T | 3,083,277 | 45 | 37 |
| T cell, unspecified | 2,970,584 | 29 | 24 |
| Enterocyte | 2,072,333 | 6 | 5 |
| Plasma cell | 1,956,982 | 43 | 41 |
Spatial analyses
Result pages show precomputed modules; Help keeps the interpretation rules.
01Spatial Domainslabel-neighborhood compartments
02Interaction Propensitydirected cell-type contacts
03Network Topologygraph architecture by label
TiersSeparated by chart; never mixed in one analytical plot
GraphPer-sample Delaunay with distance filtering
NANot available in the current release; not a biological zero
Domains
Label-only, data-driven neighborhood compartments from coordinates plus Tier 2 or Tier 3 labels.
Domain IDSample-local; D1 is not cross-study equivalent
FamilyCross-sample grouping by composition profile
TierTier 2 is stable; Tier 3 is more specific
Method and parameters
InputsCoordinates and tiered labels only
OutputsDomain summary, composition, interfaces, mixing metrics, PNG previews
CaveatData-driven label neighborhoods, not histology-confirmed regions
Interaction Propensity
Directed cell-type contacts on a sample-level spatial graph. Matrix X is from_label; Y is to_label.
DirectionA to B and B to A remain separate
ColorRed enriched; blue depleted
EngineimcRtools on distance-limited Delaunay graph
Method and parameters
InputsCoordinates, graph, Tier 3 or Tier 4 labels
Permutations100 for routine atlas updates
OutputsNative engine fields plus display-ready CSVs
Network Topology
Sample-level graph architecture after cells are grouped by curated ontology labels.
ModularityCommunity separation
AssortativitySimilar labels preferentially connect
BetweennessBridge-like role between graph regions or lineages
Method and parameters
InputsCoordinates, graph, Tier 1 through Tier 4 labels
SummariesNode centrality, degree, betweenness, lineage and bucket edges
CaveatCompare within the same graph rule and label tier first
Browse and search
Browse is both catalog and search-results workspace.
SearchDataset key, title, PMID, DOI, organ, disease, technique
Dataset viewOne row per deployed dataset
Sample viewOne row per sample, best for organ and module readiness
Dataset pages
Dataset pages are terse records for one deployed dataset.
DefaultOverview, reference, organ inclusion, sample manifest
OntologyComposition and raw-to-curated flow when available
ModulesPer-sample links to spatial and DEG results
Curated tiers
Raw labels are preserved; curated tiers add a cross-study comparison layer.
Tier 1Super-broad groups
Tier 2Broad biology
Tier 3Default cross-study comparison layer
Tier 4Source-supported detail
A valid label is not automatically a strong pooled comparison label; reuse across datasets matters.