10x Xenium
Human breast
xenium-ffpe-human-breast-biomarkers__human-breast-biomarkers-s4-mid
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 39456, 22892), (3, 19728, 11446), (3, 9864, 5723), (3, 4932, 2861), (3, 2466, 1430)
│ └── 'morphology_focus': DataTree[cyx] (4, 30832, 54080), (4, 15416, 27040), (4, 7708, 13520), (4, 3854, 6760), (4, 1927, 3380)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30832, 54080), (15416, 27040), (7708, 13520), (3854, 6760), (1927, 3380)
│ └── 'nucleus_labels': DataTree[yx] (30832, 54080), (15416, 27040), (7708, 13520), (3854, 6760), (1927, 3380)
├── Points
│ └── 'transcripts': DataFrame with shape: (132733733, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (335709, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (335709, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (342970, 2) (2D shapes)
└── Tables
└── 'table': AnnData (335709, 280)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), 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("R8L8lvXszssMJRo4") # 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/R8L8lvXszssMJRo4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid R8L8lvXszssMJRo4 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["R8L8lvXszssMJRo40001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- breast
- Modality
- RNA
- Observations
- 335,709
- Transcripts
- 132,733,733
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 22,892 × 39,456 px
- mpp
- 0.008 µm/px
- Size
- 9.9 GB
- Sample ID
- xenium-ffpe-human-breast-biomarkers__human-breast-biomarkers-s4-mid
- License
- CC BY 4.0
- Published
- Dec 11, 2025
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB