10x Xenium
Mouse lung
GSM9598485
bronze Interactive viewer pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27385, 54022), (1, 13692, 27011), (1, 6846, 13505), (1, 3423, 6752), (1, 1711, 3376)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (27295, 53262), (13647, 26631), (6823, 13315), (3411, 6657), (1705, 3328)
│ └── 'nucleus_labels': DataTree[yx] (27294, 53215), (13647, 26607), (6823, 13303), (3411, 6651), (1705, 3325)
├── Points
│ └── 'transcripts': DataFrame with shape: (135600678, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (190051, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (190051, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (190043, 2) (2D shapes)
└── Tables
└── 'table': AnnData (190051, 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("7kGCw87FN8KeRE2o0000")
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("7kGCw87FN8KeRE2o") # 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 7kGCw87FN8KeRE2o0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7kGCw87FN8KeRE2o
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7kGCw87FN8KeRE2oLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Condition
- pulmonary fibrosis
- Modality
- RNA
- Observations (cells)
- 190,051
- Transcripts
- 135,600,678
- Tier
- bronze
- Size
- 5.0 GB
- Sample ID
- GSM9598485
- License
- NCBI GEO policy
- Published
- Mar 24, 2026
Cite this dataset
doi.org/10.1126/scitranslmed.ads2673 ↗ BibTeX
@article{geo:GSM9598485,
doi = {10.1126/scitranslmed.ads2673},
title = {GSM9598485},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB