State of spatial omics
Live figures across the whole SpatialData-DB catalog, rebuilt on every data update.
5,605
datasets
173.6M
cells & cell-equivalents
121M segmented · 52.5M HD 8 µm bins
12.6M
capture spots
Visium / ST, ~1–10 cells each
36.6B
decoded transcripts
imaging assays · 737 datasets
13
technologies
15
organisms
169
tissues
4,725
H&E datasets
Catalog growth
cumulative datasets by publication year
Publication verification
43% with resolved DOI
Composition
Technology
Visium4022 · 72%
10x Xenium752 · 13%
spatial transcriptomics552 · 10%
Visium HD134 · 2%
Vizgen MERSCOPE115 · 2%
MERFISH10 · 0%
PhenoCycler-Fusion4 · 0%
spatial CUT&Tag4 · 0%
MALDI mass spectrometry imaging3 · 0%
CosMx3 · 0%
10x Atera2 · 0%
PhenoCycler2 · 0%
spatial ATAC-seq2 · 0%
Organism
human3202 · 57%
mouse2196 · 39%
rat92 · 2%
ambystoma mexicanum30 · 1%
macaque24 · 0%
crab-eating macaque20 · 0%
dog13 · 0%
pig8 · 0%
leucoraja erinaceus8 · 0%
golden hamster4 · 0%
zebra finch4 · 0%
zebrafish1 · 0%
glycine max1 · 0%
arabidopsis thaliana1 · 0%
branchiostoma floridae1 · 0%
Modality
RNA5589 · 100%
protein8 · 0%
Epigenomics6 · 0%
Metabolomics3 · 0%
Cells per dataset
observations in the default table · log scale
Segmented cells, Visium HD 8 µm bins or capture spots, depending on the technology. Each dot is a dataset; the violin shows each technology's spread.
Panel size
features measured per dataset · log scale
Targeted panels (tens to thousands of genes) trade breadth for single-cell resolution; whole-transcriptome assays measure ~20–36k genes.
Transcripts per dataset
decoded transcripts, imaging assays · log scale
Detected transcript molecules in imaging-based datasets.
Image size
largest image per dataset, megapixels · log scale
Full-resolution size of the biggest image element in each SpatialData object (H&E, DAPI / morphology, IF).
Image resolution
µm per pixel, where curated · log scale
Lower is finer. Only where the image resolution has been curated so far (mostly Visium, Visium HD and ST).
Top tissues
Top conditions