10x Xenium
Human synovial membrane of synovial joint
GSM9641127
bronze Interactive viewer oligoarticular juvenile idiopathic arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37480, 34138), (1, 18740, 17069), (1, 9370, 8534), (1, 4685, 4267), (1, 2342, 2133)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37325, 32200), (18662, 16100), (9331, 8050), (4665, 4025), (2332, 2012)
│ └── 'nucleus_labels': DataTree[yx] (37316, 31890), (18658, 15945), (9329, 7972), (4664, 3986), (2332, 1993)
├── Points
│ └── 'transcripts': DataFrame with shape: (58988061, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (60074, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (60074, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (60233, 2) (2D shapes)
└── Tables
└── 'table': AnnData (60074, 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("0YHkFKDaRTkh29Wu0000")
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("0YHkFKDaRTkh29Wu") # 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 0YHkFKDaRTkh29Wu0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/0YHkFKDaRTkh29Wu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0YHkFKDaRTkh29WuLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- synovial membrane of synovial joint
- Condition
- oligoarticular juvenile idiopathic arthritis
- Modality
- RNA
- Observations (cells)
- 60,074
- Transcripts
- 58,988,061
- Tier
- bronze
- Size
- 2.2 GB
- Sample ID
- GSM9641127
- License
- NCBI GEO policy
- Published
- Apr 2, 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