10x Xenium
Human breast
xenium-ffpe-human-breast-biomarkers__human-breast-biomarkers-s4-top
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 46370, 26717), (3, 23185, 13358), (3, 11592, 6679), (3, 5796, 3339), (3, 2898, 1669)
│ └── 'morphology_focus': DataTree[cyx] (4, 37498, 54049), (4, 18749, 27024), (4, 9374, 13512), (4, 4687, 6756), (4, 2343, 3378)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (37498, 54049), (18749, 27024), (9374, 13512), (4687, 6756), (2343, 3378)
│ └── 'nucleus_labels': DataTree[yx] (37498, 54049), (18749, 27024), (9374, 13512), (4687, 6756), (2343, 3378)
├── Points
│ └── 'transcripts': DataFrame with shape: (66374520, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (192898, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (192898, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (194381, 2) (2D shapes)
└── Tables
└── 'table': AnnData (192898, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yPN7hOjFU3JihgKS0001")
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("yPN7hOjFU3JihgKS") # 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 yPN7hOjFU3JihgKS0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yPN7hOjFU3JihgKS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yPN7hOjFU3JihgKSLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- breast
- Modality
- RNA
- Observations (cells)
- 192,898
- Transcripts
- 66,374,520
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 26,717 × 46,370 px
- mpp
- 0.008 µm/px
- Size
- 8.7 GB
- Sample ID
- xenium-ffpe-human-breast-biomarkers__human-breast-biomarkers-s4-top
- 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