Mouse spleen
GSM8047884
mouse spleen malaria 69.0 MB 2,498 spots silver H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionmalaria
Spots2,498
silver H&E
Spatial omics data,
standardized and ready to explore.
A curated, cloud-native catalog of spatial-omics datasets — one schema, every technology, linked straight to the data and interactive viewers.
8,471
datasets
16
technologies
4
modalities
15
organisms
Get started
AlphaYou don't need an account. The Python client reads the public catalog and the data directly.
- Install the client. It needs Python 3.12 or newer. The command installs the alpha release, v0.1.3, and the
mainbranch may be ahead of it. - Load a dataset by its id. Every dataset and collection page has a snippet for that page.
- Search and build cohorts with the client docs →
This is an early alpha, so datasets and features are still being added and things can change. If something looks wrong, open an issue. Using an AI agent? The client ships a CLI and an MCP server.
Install
pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" Load a dataset
from sddb import Catalog
cat = Catalog() # every published dataset
ds = cat.dataset("0yftzwYvxZpqll400000")
# a SpatialData object, cached locally
sdata = ds.to_sdata()The example loads 0yftzwYvxZpqll400000, the smallest dataset.
Featured by technology
All datasets → 
Mouse brain
GSM9489188
mouse brain 650 MB 60,038 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebrain
Cells60,038
silver NCBI GEO policy
Human skin of body
NCBI760
human skin of body skin squamous cell carcinoma 203 MB 621 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueskin of body
Conditionskin squamous cell carcinoma
Spots621
Magnification20x · 0.366 µm/px
silver H&E
Human caudate lobe of liver
GSM9324329
human caudate lobe of liver liver disorder 971 MB 466,284 bins silver H&E NCBI GEO policy
TechnologyVisium HD
Organismhuman
Tissuecaudate lobe of liver
Conditionliver disorder
Bins466,284
silver H&E NCBI GEO policy
Mouse liver
GSM9372788
mouse liver 1.4 GB 140,698 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Cells140,698
silver NCBI GEO policy
Mouse brain
Zhuang-ABCA-1.010
mouse brain 5.0 MB 8,144 cells silver Allen Institute Terms of Use
TechnologyMERFISH
Organismmouse
Tissuebrain
Cells8,144
silver Allen Institute Terms of Use
Human tonsil
S-BIAD2491:250902_Fresh_Slide4_Storageconditions_Scan1
human tonsil 3.7 GB 289,534 cells silver CC0 1.0
TechnologyPhenoCycler-Fusion
Organismhuman
Tissuetonsil
Cells289,534
silver CC0 1.0
Mouse brain
GSM6753044
mouse brain 85.1 MB 9,752 obs bronze H&E NCBI GEO policy
Technologyspatial CUT&Tag
Organismmouse
Tissuebrain
Obs9,752
bronze H&E NCBI GEO policy
Mouse kidney
2024-03-14_19h23m36s
mouse kidney 66.0 MB 15,867 obs bronze H&E
TechnologyMALDI mass spectrometry imaging
Organismmouse
Tissuekidney
Obs15,867
bronze H&E
Human tonsil
protein_tonsil_25
human tonsil 1.3 GB 1,464,516 cells silver Bruker terms of use (pending review)
TechnologyCosMx
Organismhuman
Tissuetonsil
Cells1,464,516
silver Bruker terms of use (pending review)
Human breast
atera-wta-ffpe-human-breast-cancer
human breast breast cancer 24.2 GB 170,057 cells silver
Technology10x Atera
Organismhuman
Tissuebreast
Conditionbreast cancer
Cells170,057
silver
Human pancreas
S-BIAD859:6371v1:reg002
human pancreas type 1 diabetes mellitus 2.1 GB 57,248 cells silver CC0 1.0
TechnologyPhenoCycler
Organismhuman
Tissuepancreas
Conditiontype 1 diabetes mellitus
Cells57,248
silver CC0 1.0
Mouse brain
GSM6753043
mouse brain 44.3 MB 9,215 obs bronze H&E NCBI GEO policy
Technologyspatial ATAC-seq
Organismmouse
Tissuebrain
Obs9,215
bronze H&E NCBI GEO policy