10x Xenium
Mouse cerebral cortex
GSM8072117
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27462, 42671), (1, 13731, 21335), (1, 6865, 10667), (1, 3432, 5333), (1, 1716, 2666)
├── Points
│ └── 'transcripts': DataFrame with shape: (7265683, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (126119, 2) (2D shapes)
└── Tables
└── 'table': AnnData (126119, 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("83u0p0HvNESf793n0000")
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("83u0p0HvNESf793n") # 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 83u0p0HvNESf793n0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/83u0p0HvNESf793n
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 83u0p0HvNESf793nLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- cerebral cortex
- Modality
- RNA
- Observations (cells)
- 126,119
- Transcripts
- 7,265,683
- Tier
- bronze
- Size
- 1.9 GB
- Sample ID
- GSM8072117
- License
- NCBI GEO policy
- Published
- Mar 5, 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