10x Xenium
Human colon
xenium-human-colon-cancer-p2-crc-addon
silver Interactive viewer colorectal cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 34224, 31395), (4, 17112, 15697), (4, 8556, 7848), (4, 4278, 3924), (4, 2139, 1962)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34224, 31395), (17112, 15697), (8556, 7848), (4278, 3924), (2139, 1962)
│ └── 'nucleus_labels': DataTree[yx] (34224, 31395), (17112, 15697), (8556, 7848), (4278, 3924), (2139, 1962)
├── Points
│ └── 'transcripts': DataFrame with shape: (66248117, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (340837, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (340837, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (345246, 2) (2D shapes)
└── Tables
└── 'table': AnnData (340837, 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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ODlV9hhd8502waGR0000")
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("ODlV9hhd8502waGR") # 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 ODlV9hhd8502waGR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ODlV9hhd8502waGR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ODlV9hhd8502waGRLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- colon
- Condition
- colorectal cancer
- Modality
- RNA
- Observations (cells)
- 340,837
- Transcripts
- 66,248,117
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 8.6 GB
- Sample ID
- xenium-human-colon-cancer-p2-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