10x Xenium
Mouse ovary
GSM9786073
bronze Interactive viewer primary ovarian failure Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 84960, 42671), (1, 42480, 21335), (1, 21240, 10667), (1, 10620, 5333), (1, 5310, 2666)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (84365, 42023), (42182, 21011), (21091, 10505), (10545, 5252), (5272, 2626)
│ └── 'nucleus_labels': DataTree[yx] (84322, 41179), (42161, 20589), (21080, 10294), (10540, 5147), (5270, 2573)
├── Points
│ └── 'transcripts': DataFrame with shape: (334823578, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (544026, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (544026, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (549264, 2) (2D shapes)
└── Tables
└── 'table': AnnData (544026, 5006)
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("JRK5pgfURMFoGQ2k0000")
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("JRK5pgfURMFoGQ2k") # 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 JRK5pgfURMFoGQ2k0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JRK5pgfURMFoGQ2k
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JRK5pgfURMFoGQ2kLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- ovary
- Condition
- primary ovarian failure
- Modality
- RNA
- Observations (cells)
- 544,026
- Transcripts
- 334,823,578
- Tier
- bronze
- Size
- 9.8 GB
- Sample ID
- GSM9786073
- License
- NCBI GEO policy
- Published
- Jul 15, 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