10x Xenium
Mouse tongue
GSM9096728
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13718, 19976), (1, 6859, 9988), (1, 3429, 4994), (1, 1714, 2497), (1, 857, 1248)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13364, 19549), (6682, 9774), (3341, 4887), (1670, 2443), (835, 1221)
│ └── 'nucleus_labels': DataTree[yx] (12105, 18663), (6052, 9331), (3026, 4665), (1513, 2332), (756, 1166)
├── Points
│ └── 'transcripts': DataFrame with shape: (50545124, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (37590, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (37590, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (36995, 2) (2D shapes)
└── Tables
└── 'table': AnnData (37590, 5046)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("UUb8pVN0ZRhlIkzi") # 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/UUb8pVN0ZRhlIkzi
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UUb8pVN0ZRhlIkzi Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["UUb8pVN0ZRhlIkzi0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- tongue
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 37,590
- Transcripts
- 50,545,124
- Tier
- bronze
- Size
- 1.2 GB
- Sample ID
- GSM9096728
- License
- unknown
- Published
- Jul 9, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB