10x Xenium
Mouse brain
GSM8257563
bronze Interactive viewer glioblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13720, 22770), (1, 6860, 11385), (1, 3430, 5692), (1, 1715, 2846), (1, 857, 1423)
├── Points
│ └── 'transcripts': DataFrame with shape: (4755609, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (37985, 2) (2D shapes)
└── Tables
└── 'table': AnnData (37985, 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("9cvzFsY8Bvg7j4lF0000")
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("9cvzFsY8Bvg7j4lF") # 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 9cvzFsY8Bvg7j4lF0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9cvzFsY8Bvg7j4lF
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9cvzFsY8Bvg7j4lFLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- glioblastoma
- Modality
- RNA
- Observations (cells)
- 37,985
- Transcripts
- 4,755,609
- Tier
- bronze
- Size
- 574 MB
- Sample ID
- GSM8257563
- 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