10x Xenium
Human synovial membrane of synovial joint
GSM9641122
bronze Interactive viewer oligoarticular juvenile idiopathic arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30685, 39782), (1, 15342, 19891), (1, 7671, 9945), (1, 3835, 4972), (1, 1917, 2486)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (28427, 37660), (14213, 18830), (7106, 9415), (3553, 4707), (1776, 2353)
│ └── 'nucleus_labels': DataTree[yx] (27883, 37270), (13941, 18635), (6970, 9317), (3485, 4658), (1742, 2329)
├── Points
│ └── 'transcripts': DataFrame with shape: (14993332, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (19922, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (19922, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (19872, 2) (2D shapes)
└── Tables
└── 'table': AnnData (19922, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ni9HcHL3xgr908UE") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ni9HcHL3xgr908UE
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ni9HcHL3xgr908UE Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ni9HcHL3xgr908UE0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- synovial membrane of synovial joint
- Condition
- oligoarticular juvenile idiopathic arthritis
- Modality
- RNA
- Observations
- 19,922
- Transcripts
- 14,993,332
- Tier
- bronze
- Size
- 867 MB
- Sample ID
- GSM9641122
- License
- unknown
- Published
- Apr 2, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB