10x Xenium
Human lymph node
preview-data-xenium-prime-gene-expression
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 30987, 28915), (3, 15493, 14457), (3, 7746, 7228), (3, 3873, 3614), (3, 1936, 1807)
│ └── 'morphology_focus': DataTree[cyx] (4, 34119, 39776), (4, 17059, 19888), (4, 8529, 9944), (4, 4264, 4972), (4, 2132, 2486)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34119, 39776), (17059, 19888), (8529, 9944), (4264, 4972), (2132, 2486)
│ └── 'nucleus_labels': DataTree[yx] (34119, 39776), (17059, 19888), (8529, 9944), (4264, 4972), (2132, 2486)
├── Points
│ └── 'transcripts': DataFrame with shape: (232650139, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (708983, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (708983, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (749594, 2) (2D shapes)
└── Tables
└── 'table': AnnData (708983, 4624)
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("BXFR9f1Oozo97Tka0001")
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("BXFR9f1Oozo97Tka") # 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 BXFR9f1Oozo97Tka0001 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/BXFR9f1Oozo97Tka
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid BXFR9f1Oozo97TkaLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lymph node
- Modality
- RNA
- Observations (cells)
- 708,983
- Transcripts
- 232,650,139
- Tier
- silver
- Chemistry
- Xenium Prime
- Magnification
- 40x
- Resolution
- 28,915 × 30,987 px
- mpp
- 0.007 µm/px
- Size
- 15.5 GB
- Sample ID
- preview-data-xenium-prime-gene-expression
- License
- CC BY 4.0
- Published
- May 28, 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