10x Xenium
Mouse brain
GSM8257573
bronze Interactive viewer glioblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20503, 22790), (1, 10251, 11395), (1, 5125, 5697), (1, 2562, 2848), (1, 1281, 1424)
├── Points
│ └── 'transcripts': DataFrame with shape: (18334991, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (134142, 2) (2D shapes)
└── Tables
└── 'table': AnnData (134142, 347)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("SOUcjQpY9uUkeiRI0000")
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("SOUcjQpY9uUkeiRI") # 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 SOUcjQpY9uUkeiRI0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/SOUcjQpY9uUkeiRI
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid SOUcjQpY9uUkeiRILicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- glioblastoma
- Modality
- RNA
- Observations (cells)
- 134,142
- Transcripts
- 18,334,991
- Tier
- bronze
- Size
- 1.4 GB
- Sample ID
- GSM8257573
- License
- NCBI GEO policy
- Published
- Aug 10, 2024
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