10x Xenium
Mouse lung
GSM9598487
bronze Interactive viewer pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23990, 48346), (1, 11995, 24173), (1, 5997, 12086), (1, 2998, 6043), (1, 1499, 3021)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (23913, 46780), (11956, 23390), (5978, 11695), (2989, 5847), (1494, 2923)
│ └── 'nucleus_labels': DataTree[yx] (23870, 46755), (11935, 23377), (5967, 11688), (2983, 5844), (1491, 2922)
├── Points
│ └── 'transcripts': DataFrame with shape: (123867874, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (155374, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (155374, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (155373, 2) (2D shapes)
└── Tables
└── 'table': AnnData (155374, 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("0F4R15XBqM1fhQFi0000")
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("0F4R15XBqM1fhQFi") # 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 0F4R15XBqM1fhQFi0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/0F4R15XBqM1fhQFi
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0F4R15XBqM1fhQFiLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- lung
- Condition
- pulmonary fibrosis
- Modality
- RNA
- Observations (cells)
- 155,374
- Transcripts
- 123,867,874
- Tier
- bronze
- Size
- 4.4 GB
- Sample ID
- GSM9598487
- License
- NCBI GEO policy
- Published
- Mar 24, 2026
Cite this dataset
doi.org/10.1126/scitranslmed.ads2673 ↗ BibTeX
@article{geo:GSM9598487,
doi = {10.1126/scitranslmed.ads2673},
title = {GSM9598487},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB