10x Xenium
Human synovial membrane of synovial joint
GSM9641125
bronze Interactive viewer rheumatoid factor-negative juvenile idiopathic arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 61219, 39831), (1, 30609, 19915), (1, 15304, 9957), (1, 7652, 4978), (1, 3826, 2489)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (58443, 39635), (29221, 19817), (14610, 9908), (7305, 4954), (3652, 2477)
│ └── 'nucleus_labels': DataTree[yx] (58418, 39585), (29209, 19792), (14604, 9896), (7302, 4948), (3651, 2474)
├── Points
│ └── 'transcripts': DataFrame with shape: (66638512, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (131542, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (131542, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (132430, 2) (2D shapes)
└── Tables
└── 'table': AnnData (131542, 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("qlbEHk7rrIUvlVCU") # 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/qlbEHk7rrIUvlVCU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qlbEHk7rrIUvlVCU Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["qlbEHk7rrIUvlVCU0000"])[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
- 131,542
- Transcripts
- 66,638,512
- Tier
- bronze
- Size
- 3.2 GB
- Sample ID
- GSM9641125
- 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