10x Xenium
Human ovary
xenium-comparison-fresh-frozen-human-ovarian-cancer__human-ovary-cancer-ff
silver Interactive viewer H&E ovarian cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 57040, 51442), (3, 28520, 25721), (3, 14260, 12860), (3, 7130, 6430), (3, 3565, 3215)
│ └── 'morphology_focus': DataTree[cyx] (4, 34184, 36968), (4, 17092, 18484), (4, 8546, 9242), (4, 4273, 4621), (4, 2136, 2310)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34184, 36968), (17092, 18484), (8546, 9242), (4273, 4621), (2136, 2310)
│ └── 'nucleus_labels': DataTree[yx] (34184, 36968), (17092, 18484), (8546, 9242), (4273, 4621), (2136, 2310)
├── Points
│ └── 'transcripts': DataFrame with shape: (184281542, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (205082, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (205082, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (210467, 2) (2D shapes)
└── Tables
└── 'table': AnnData (205082, 477)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), morphology_focus (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("d4yjKUQ98oi2aGPT0001")
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("d4yjKUQ98oi2aGPT") # 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 d4yjKUQ98oi2aGPT0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/d4yjKUQ98oi2aGPT
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid d4yjKUQ98oi2aGPTLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ovary
- Condition
- ovarian cancer
- Modality
- RNA
- Observations (cells)
- 205,082
- Transcripts
- 184,281,542
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 51,442 × 57,040 px
- mpp
- 0.004 µm/px
- Size
- 17.8 GB
- Sample ID
- xenium-comparison-fresh-frozen-human-ovarian-cancer__human-ovary-cancer-ff
- License
- CC BY 4.0
- Published
- Oct 7, 2025
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB