10x Xenium
Human synovial membrane of synovial joint
GSM9879488
silver Interactive viewer juvenile idiopathic arthritis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 44251, 53941), (1, 22125, 26970), (1, 11062, 13485), (1, 5531, 6742), (1, 2765, 3371)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (40582, 53728), (20291, 26864), (10145, 13432), (5072, 6716), (2536, 3358)
│ └── 'nucleus_labels': DataTree[yx] (40565, 53712), (20282, 26856), (10141, 13428), (5070, 6714), (2535, 3357)
├── Points
│ └── 'transcripts': DataFrame with shape: (32803169, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38514, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38514, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38570, 2) (2D shapes)
└── Tables
└── 'table': AnnData (38514, 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("8xQJZP67izRGswYT") # 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/8xQJZP67izRGswYT
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8xQJZP67izRGswYT Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["8xQJZP67izRGswYT0000"])[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
- 38,514
- Transcripts
- 32,803,169
- Tier
- silver
- Size
- 2.0 GB
- Sample ID
- GSM9879488
- 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