10x Xenium
Mouse lung
GSM9598488
bronze Interactive viewer pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27379, 51210), (1, 13689, 25605), (1, 6844, 12802), (1, 3422, 6401), (1, 1711, 3200)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (27278, 51203), (13639, 25601), (6819, 12800), (3409, 6400), (1704, 3200)
│ └── 'nucleus_labels': DataTree[yx] (27255, 49832), (13627, 24916), (6813, 12458), (3406, 6229), (1703, 3114)
├── Points
│ └── 'transcripts': DataFrame with shape: (146953183, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (195291, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (195291, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (195306, 2) (2D shapes)
└── Tables
└── 'table': AnnData (195291, 5006)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (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("Nb8CJozstIMhsFoV0000")
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("Nb8CJozstIMhsFoV") # 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 Nb8CJozstIMhsFoV0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Nb8CJozstIMhsFoV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Nb8CJozstIMhsFoVLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Condition
- pulmonary fibrosis
- Modality
- RNA
- Observations (cells)
- 195,291
- Transcripts
- 146,953,183
- Tier
- bronze
- Size
- 5.2 GB
- Sample ID
- GSM9598488
- License
- NCBI GEO policy
- Published
- Mar 24, 2026
Cite this dataset
doi.org/10.1126/scitranslmed.ads2673 ↗ BibTeX
@article{geo:GSM9598488,
doi = {10.1126/scitranslmed.ads2673},
title = {GSM9598488},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB