10x Xenium
Human skin of body
GSM9451456
silver Interactive viewer melanoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 10326, 14315), (1, 5163, 7157), (1, 2581, 3578), (1, 1290, 1789), (1, 645, 894)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (9622, 11890), (4811, 5945), (2405, 2972), (1202, 1486), (601, 743)
│ └── 'nucleus_labels': DataTree[yx] (9601, 11857), (4800, 5928), (2400, 2964), (1200, 1482), (600, 741)
├── Points
│ └── 'transcripts': DataFrame with shape: (18814932, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (47962, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (47962, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (49301, 2) (2D shapes)
└── Tables
└── 'table': AnnData (47962, 5001)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ydF7XXLo2DbDRjDm0000")
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("ydF7XXLo2DbDRjDm") # 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 ydF7XXLo2DbDRjDm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ydF7XXLo2DbDRjDm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ydF7XXLo2DbDRjDmLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- skin of body
- Condition
- melanoma
- Modality
- RNA
- Observations (cells)
- 47,962
- Transcripts
- 18,814,932
- Tier
- silver
- Size
- 612 MB
- Sample ID
- GSM9451456
- License
- NCBI GEO policy
- Published
- Sep 8, 2026
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