10x Xenium
Mouse intestine
GSM8605283
bronze Interactive viewer melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37458, 51069), (1, 18729, 25534), (1, 9364, 12767), (1, 4682, 6383), (1, 2341, 3191)
├── Labels
│ └── 'cell_labels': DataTree[yx] (37067, 50822), (18533, 25411), (9266, 12705), (4633, 6352), (2316, 3176)
├── Points
│ └── 'transcripts': DataFrame with shape: (61620088, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (315017, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (315017, 2) (2D shapes)
└── Tables
└── 'table': AnnData (315017, 399)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("PZpv9768J7w60vW3") # 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/PZpv9768J7w60vW3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PZpv9768J7w60vW3 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["PZpv9768J7w60vW30000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- intestine
- Condition
- melanoma
- Modality
- RNA
- Observations
- 315,017
- Transcripts
- 61,620,088
- Tier
- bronze
- Size
- 4.5 GB
- Sample ID
- GSM8605283
- License
- unknown
- Published
- Jan 14, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB