10x Xenium
Human synovial membrane of synovial joint
GSM9879487
silver Interactive viewer juvenile idiopathic arthritis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 54446, 54016), (1, 27223, 27008), (1, 13611, 13504), (1, 6805, 6752), (1, 3402, 3376)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (53443, 52338), (26721, 26169), (13360, 13084), (6680, 6542), (3340, 3271)
│ └── 'nucleus_labels': DataTree[yx] (53416, 52322), (26708, 26161), (13354, 13080), (6677, 6540), (3338, 3270)
├── Points
│ └── 'transcripts': DataFrame with shape: (27198448, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (37295, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (37295, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (37231, 2) (2D shapes)
└── Tables
└── 'table': AnnData (37295, 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("FYXqijLl2jEusxVV") # 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/FYXqijLl2jEusxVV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FYXqijLl2jEusxVV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["FYXqijLl2jEusxVV0000"])[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
- juvenile idiopathic arthritis
- Modality
- RNA
- Observations
- 37,295
- Transcripts
- 27,198,448
- Tier
- silver
- Size
- 1.9 GB
- Sample ID
- GSM9879487
- License
- unknown
- Published
- Sep 22, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB