10x Xenium
Human lung
GSM9358874
bronze Interactive viewer chronic obstructive pulmonary disease Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 95274, 42858), (1, 47637, 21429), (1, 23818, 10714), (1, 11909, 5357), (1, 5954, 2678)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (94980, 41851), (47490, 20925), (23745, 10462), (11872, 5231), (5936, 2615)
│ └── 'nucleus_labels': DataTree[yx] (94784, 38939), (47392, 19469), (23696, 9734), (11848, 4867), (5924, 2433)
├── Points
│ └── 'transcripts': DataFrame with shape: (18463299, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (219246, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (219246, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (219046, 2) (2D shapes)
└── Tables
└── 'table': AnnData (219246, 480)
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("Z1iFoCSHa9kIQlGC0000")
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("Z1iFoCSHa9kIQlGC") # 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 Z1iFoCSHa9kIQlGC0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Z1iFoCSHa9kIQlGC
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Z1iFoCSHa9kIQlGCLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- chronic obstructive pulmonary disease
- Modality
- RNA
- Observations (cells)
- 219,246
- Transcripts
- 18,463,299
- Tier
- bronze
- Size
- 4.5 GB
- Sample ID
- GSM9358874
- License
- NCBI GEO policy
- Published
- Dec 9, 2025
Cite this dataset
doi.org/10.1038/s41588-025-02480-z ↗ BibTeX
@article{geo:GSM9358874,
doi = {10.1038/s41588-025-02480-z},
title = {GSM9358874},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB