10x Xenium
Mouse lung
GSM9598483
bronze Interactive viewer pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20562, 45517), (1, 10281, 22758), (1, 5140, 11379), (1, 2570, 5689), (1, 1285, 2844)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20493, 44158), (10246, 22079), (5123, 11039), (2561, 5519), (1280, 2759)
│ └── 'nucleus_labels': DataTree[yx] (20443, 44129), (10221, 22064), (5110, 11032), (2555, 5516), (1277, 2758)
├── Points
│ └── 'transcripts': DataFrame with shape: (164446332, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (291427, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (291427, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (291750, 2) (2D shapes)
└── Tables
└── 'table': AnnData (291427, 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("RGwTN0GjpLmRHEhA0000")
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("RGwTN0GjpLmRHEhA") # 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 RGwTN0GjpLmRHEhA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/RGwTN0GjpLmRHEhA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid RGwTN0GjpLmRHEhALicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Condition
- pulmonary fibrosis
- Modality
- RNA
- Observations (cells)
- 291,427
- Transcripts
- 164,446,332
- Tier
- bronze
- Size
- 5.2 GB
- Sample ID
- GSM9598483
- License
- NCBI GEO policy
- Published
- Mar 24, 2026
Cite this dataset
doi.org/10.1126/scitranslmed.ads2673 ↗ BibTeX
@article{geo:GSM9598483,
doi = {10.1126/scitranslmed.ads2673},
title = {GSM9598483},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB