10x Xenium
Human breast
GSM9509166
bronze Interactive viewer breast cancer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (1, 17092, 25596), (1, 8546, 12798), (1, 4273, 6399), (1, 2136, 3199), (1, 1068, 1599)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (16981, 23899), (8490, 11949), (4245, 5974), (2122, 2987), (1061, 1493)
│ └── 'nucleus_labels': DataTree[yx] (16862, 23759), (8431, 11879), (4215, 5939), (2107, 2969), (1053, 1484)
├── Points
│ └── 'transcripts': DataFrame with shape: (19335897, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (98449, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (98449, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (98449, 1) (2D shapes)
└── Tables
└── 'table': AnnData (98449, 280)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("mQWrnW24rhj81dpW0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("mQWrnW24rhj81dpW") # stem uid: Lamin resolves it to the latest version
sdata = artifact.load() # cache, then load into memory
group = artifact.open() # stream without downloading
path = artifact.cache() # sync into the local cache, returns the path Shell
# sddb client: download the .zarr into data/
sddb-cli download mQWrnW24rhj81dpW0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/mQWrnW24rhj81dpW
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mQWrnW24rhj81dpWLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (cells)
- 98,449
- Transcripts
- 19,335,897
- Tier
- bronze
- Size
- 1.3 GB
- Sample ID
- GSM9509166
- License
- NCBI GEO policy
- Published
- Mar 27, 2026
Cite this dataset
doi.org/10.1038/s41592-026-03089-8 ↗ BibTeX
@article{geo:GSM9509166,
doi = {10.1038/s41592-026-03089-8},
title = {GSM9509166},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB