10x Xenium
Mouse kidney
GSM8717006
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37532, 54032), (1, 18766, 27016), (1, 9383, 13508), (1, 4691, 6754), (1, 2345, 3377)
├── Points
│ └── 'transcripts': DataFrame with shape: (140072580, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (397721, 2) (2D shapes)
└── Tables
└── 'table': AnnData (397721, 479)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("nWObj5iNaX2P3kSl0000")
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("nWObj5iNaX2P3kSl") # 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 nWObj5iNaX2P3kSl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/nWObj5iNaX2P3kSl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid nWObj5iNaX2P3kSlLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- kidney
- Modality
- RNA
- Observations (cells)
- 397,721
- Transcripts
- 140,072,580
- Tier
- silver
- Size
- 6.9 GB
- Sample ID
- GSM8717006
- License
- NCBI GEO policy
- Published
- Jan 13, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB