10x Xenium
Human colon
xenium-human-colon-cancer-p5-crc-addon
silver Interactive viewer colorectal cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 30874, 31470), (4, 15437, 15735), (4, 7718, 7867), (4, 3859, 3933), (4, 1929, 1966)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30874, 31470), (15437, 15735), (7718, 7867), (3859, 3933), (1929, 1966)
│ └── 'nucleus_labels': DataTree[yx] (30874, 31470), (15437, 15735), (7718, 7867), (3859, 3933), (1929, 1966)
├── Points
│ └── 'transcripts': DataFrame with shape: (46255601, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (275998, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (275998, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (269331, 2) (2D shapes)
└── Tables
└── 'table': AnnData (275998, 422)
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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("HOoZeyrVaBDC3qRR") # 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/HOoZeyrVaBDC3qRR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid HOoZeyrVaBDC3qRR Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["HOoZeyrVaBDC3qRR0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- colon
- Condition
- colorectal cancer
- Modality
- RNA
- Observations
- 275,998
- Transcripts
- 46,255,601
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 7.5 GB
- Sample ID
- xenium-human-colon-cancer-p5-crc-addon
- License
- CC BY 4.0
- Published
- Mar 5, 2024
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