10x Xenium
Human bone marrow
GSM9228906
silver Interactive viewer plasma cell myeloma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 30673, 28466), (4, 15336, 14233), (4, 7668, 7116), (4, 3834, 3558), (4, 1917, 1779)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (28913, 27954), (14456, 13977), (7228, 6988), (3614, 3494), (1807, 1747)
│ └── 'nucleus_labels': DataTree[yx] (28890, 27591), (14445, 13795), (7222, 6897), (3611, 3448), (1805, 1724)
├── Points
│ └── 'transcripts': DataFrame with shape: (4055637, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (35664, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (35664, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (35926, 2) (2D shapes)
└── Tables
└── 'table': AnnData (35664, 480)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("uifjEUsCzR4N8brV") # 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/uifjEUsCzR4N8brV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid uifjEUsCzR4N8brV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["uifjEUsCzR4N8brV0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Condition
- plasma cell myeloma
- Modality
- RNA
- Observations
- 35,664
- Transcripts
- 4,055,637
- Tier
- silver
- Size
- 2.0 GB
- Sample ID
- GSM9228906
- License
- unknown
- Published
- Sep 14, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB