10x Xenium
Human oral cavity
GSM9054488
bronze Interactive viewer ameloblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 17119, 19988), (1, 8559, 9994), (1, 4279, 4997), (1, 2139, 2498), (1, 1069, 1249)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17010, 19981), (8505, 9990), (4252, 4995), (2126, 2497), (1063, 1248)
│ └── 'nucleus_labels': DataTree[yx] (16988, 19961), (8494, 9980), (4247, 4990), (2123, 2495), (1061, 1247)
├── Points
│ └── 'transcripts': DataFrame with shape: (13813952, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38672, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38672, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38312, 2) (2D shapes)
└── Tables
└── 'table': AnnData (38672, 476)
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("YXG4wYiPg5ELCVLV") # 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/YXG4wYiPg5ELCVLV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YXG4wYiPg5ELCVLV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["YXG4wYiPg5ELCVLV0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- oral cavity
- Condition
- ameloblastoma
- Modality
- RNA
- Observations
- 38,672
- Transcripts
- 13,813,952
- Tier
- bronze
- Size
- 892 MB
- Sample ID
- GSM9054488
- License
- unknown
- Published
- Aug 6, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB