10x Xenium
Human synovial membrane of synovial joint
GSM9641126
bronze Interactive viewer rheumatoid factor-negative juvenile idiopathic arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 51031, 48307), (1, 25515, 24153), (1, 12757, 12076), (1, 6378, 6038), (1, 3189, 3019)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (50425, 48054), (25212, 24027), (12606, 12013), (6303, 6006), (3151, 3003)
│ └── 'nucleus_labels': DataTree[yx] (48050, 48007), (24025, 24003), (12012, 12001), (6006, 6000), (3003, 3000)
├── Points
│ └── 'transcripts': DataFrame with shape: (68471502, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (78203, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (78203, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (78450, 2) (2D shapes)
└── Tables
└── 'table': AnnData (78203, 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("JAmf2Hy4ZExaiuep") # 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/JAmf2Hy4ZExaiuep
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JAmf2Hy4ZExaiuep Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["JAmf2Hy4ZExaiuep0000"])[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
- rheumatoid factor-negative juvenile idiopathic arthritis
- Modality
- RNA
- Observations
- 78,203
- Transcripts
- 68,471,502
- Tier
- bronze
- Size
- 2.6 GB
- Sample ID
- GSM9641126
- 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