10x Xenium
Human breast
ffpe-human-breast-with-pre-designed-panel-1-standard__ffpe-human-breast-ilc
silver Interactive viewer breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 41405, 48511), (1, 20702, 24255), (1, 10351, 12127), (1, 5175, 6063), (1, 2587, 3031)
│ └── 'morphology_mip': DataTree[cyx] (1, 41405, 48511), (1, 20702, 24255), (1, 10351, 12127), (1, 5175, 6063), (1, 2587, 3031)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (41405, 48511), (20702, 24255), (10351, 12127), (5175, 6063), (2587, 3031)
│ └── 'nucleus_labels': DataTree[yx] (41405, 48511), (20702, 24255), (10351, 12127), (5175, 6063), (2587, 3031)
├── Points
│ └── 'transcripts': DataFrame with shape: (43775350, 8) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (356746, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (356746, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (356746, 1) (2D shapes)
└── Tables
└── 'table': AnnData (356746, 280)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), 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("lIdqctN6dzjTuvts0000")
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("lIdqctN6dzjTuvts") # 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 lIdqctN6dzjTuvts0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/lIdqctN6dzjTuvts
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lIdqctN6dzjTuvtsLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (cells)
- 356,746
- Transcripts
- 43,775,350
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 6.2 GB
- Sample ID
- ffpe-human-breast-with-pre-designed-panel-1-standard__ffpe-human-breast-ilc
- License
- CC BY 4.0
- Published
- Jan 22, 2023
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