10x Xenium
Human ovary
xenium-prime-fresh-frozen-human-ovary
silver Interactive viewer H&E adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 41263, 78928), (3, 20631, 39464), (3, 10315, 19732), (3, 5157, 9866), (3, 2578, 4933)
│ └── 'morphology_focus': DataTree[cyx] (4, 101928, 54013), (4, 50964, 27006), (4, 25482, 13503), (4, 12741, 6751), (4, 6370, 3375)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (101928, 54013), (50964, 27006), (25482, 13503), (12741, 6751), (6370, 3375)
│ └── 'nucleus_labels': DataTree[yx] (101928, 54013), (50964, 27006), (25482, 13503), (12741, 6751), (6370, 3375)
├── Points
│ └── 'transcripts': DataFrame with shape: (2698510033, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1157659, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (1157659, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (1148378, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1157659, 5001)
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("U8NS7yFoxtrKiGJO0001")
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("U8NS7yFoxtrKiGJO") # 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 U8NS7yFoxtrKiGJO0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/U8NS7yFoxtrKiGJO
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid U8NS7yFoxtrKiGJOLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- ovary
- Condition
- adenocarcinoma
- Modality
- RNA
- Observations (cells)
- 1,157,659
- Transcripts
- 2,698,510,033
- Tier
- silver
- Chemistry
- Xenium Prime
- Magnification
- 40x
- Resolution
- 78,928 × 41,263 px
- mpp
- 0.004 µm/px
- Size
- 95.5 GB
- Sample ID
- xenium-prime-fresh-frozen-human-ovary
- License
- CC BY 4.0
- Published
- Sep 4, 2024
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