10x Xenium
Human brain
GSM9617482
silver Interactive viewer breast carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 51026, 51110), (1, 25513, 25555), (1, 12756, 12777), (1, 6378, 6388), (1, 3189, 3194)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (51025, 51109), (25512, 25554), (12756, 12777), (6378, 6388), (3189, 3194)
│ └── 'nucleus_labels': DataTree[yx] (50992, 51086), (25496, 25543), (12748, 12771), (6374, 6385), (3187, 3192)
├── Points
│ └── 'transcripts': DataFrame with shape: (94732014, 9) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (386809, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (386809, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (386809, 1) (2D shapes)
└── Tables
└── 'table': AnnData (386809, 280)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("YT5ZxeOG5iGgWroU0000")
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("YT5ZxeOG5iGgWroU") # 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 YT5ZxeOG5iGgWroU0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/YT5ZxeOG5iGgWroU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid YT5ZxeOG5iGgWroULicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- breast carcinoma
- Modality
- RNA
- Observations (cells)
- 386,809
- Transcripts
- 94,732,014
- Tier
- silver
- Size
- 6.1 GB
- Sample ID
- GSM9617482
- License
- NCBI GEO policy
- Published
- May 23, 2026
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