10x Xenium
Human kidney
GSM8216268
bronze Interactive viewer IgA glomerulonephritis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37457, 8651), (1, 18728, 4325), (1, 9364, 2162), (1, 4682, 1081), (1, 2341, 540)
├── Points
│ └── 'transcripts': DataFrame with shape: (3813412, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (30802, 2) (2D shapes)
└── Tables
└── 'table': AnnData (30802, 377)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("W1bZvhwcfHpd4PID") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/W1bZvhwcfHpd4PID
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid W1bZvhwcfHpd4PID Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["W1bZvhwcfHpd4PID0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- IgA glomerulonephritis
- Modality
- RNA
- Observations
- 30,802
- Transcripts
- 3,813,412
- Tier
- bronze
- Size
- 463 MB
- Sample ID
- GSM8216268
- License
- unknown
- Published
- Apr 23, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB