10x Xenium
Human breast
GSM9509158
bronze Interactive viewer breast cancer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (1, 17115, 22798), (1, 8557, 11399), (1, 4278, 5699), (1, 2139, 2849), (1, 1069, 1424)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (15497, 19864), (7748, 9932), (3874, 4966), (1937, 2483), (968, 1241)
│ └── 'nucleus_labels': DataTree[yx] (15357, 19726), (7678, 9863), (3839, 4931), (1919, 2465), (959, 1232)
├── Points
│ └── 'transcripts': DataFrame with shape: (2473905, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38610, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38610, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38610, 1) (2D shapes)
└── Tables
└── 'table': AnnData (38610, 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("pJrkEtq1aDQxvbzk0000")
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("pJrkEtq1aDQxvbzk") # 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 pJrkEtq1aDQxvbzk0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pJrkEtq1aDQxvbzk
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pJrkEtq1aDQxvbzkLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (cells)
- 38,610
- Transcripts
- 2,473,905
- Tier
- bronze
- Size
- 636 MB
- Sample ID
- GSM9509158
- License
- NCBI GEO policy
- Published
- Mar 27, 2026
Cite this dataset
doi.org/10.1038/s41592-026-03089-8 ↗ BibTeX
@article{geo:GSM9509158,
doi = {10.1038/s41592-026-03089-8},
title = {GSM9509158},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB