10x Xenium
Human bone marrow
GSM9228907
silver Interactive viewer plasma cell myeloma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 34085, 42589), (4, 17042, 21294), (4, 8521, 10647), (4, 4260, 5323), (4, 2130, 2661)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (33679, 42519), (16839, 21259), (8419, 10629), (4209, 5314), (2104, 2657)
│ └── 'nucleus_labels': DataTree[yx] (33671, 42485), (16835, 21242), (8417, 10621), (4208, 5310), (2104, 2655)
├── Points
│ └── 'transcripts': DataFrame with shape: (14773048, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (73464, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (73464, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (74593, 2) (2D shapes)
└── Tables
└── 'table': AnnData (73464, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("I7QHYPOCmrWyQzUL0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("I7QHYPOCmrWyQzUL") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download I7QHYPOCmrWyQzUL0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/I7QHYPOCmrWyQzUL
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid I7QHYPOCmrWyQzULLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Condition
- plasma cell myeloma
- Modality
- RNA
- Observations (cells)
- 73,464
- Transcripts
- 14,773,048
- Tier
- silver
- Size
- 5.1 GB
- Sample ID
- GSM9228907
- License
- NCBI GEO policy
- Published
- Sep 14, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB