10x Xenium
Human lung
human-lung-cancer-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard
silver Interactive viewer lung cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 13754, 51108), (1, 6877, 25554), (1, 3438, 12777), (1, 1719, 6388), (1, 859, 3194)
│ └── 'morphology_mip': DataTree[cyx] (1, 13754, 51108), (1, 6877, 25554), (1, 3438, 12777), (1, 1719, 6388), (1, 859, 3194)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13754, 51108), (6877, 25554), (3438, 12777), (1719, 6388), (859, 3194)
│ └── 'nucleus_labels': DataTree[yx] (13754, 51108), (6877, 25554), (3438, 12777), (1719, 6388), (859, 3194)
├── Points
│ └── 'transcripts': DataFrame with shape: (30556489, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (150365, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (150365, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (150365, 1) (2D shapes)
└── Tables
└── 'table': AnnData (150365, 377)
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("1rooDV3jrEYzgsdz0000")
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("1rooDV3jrEYzgsdz") # 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 1rooDV3jrEYzgsdz0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1rooDV3jrEYzgsdz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1rooDV3jrEYzgsdzLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- lung cancer
- Modality
- RNA
- Observations (cells)
- 150,365
- Transcripts
- 30,556,489
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 3.4 GB
- Sample ID
- human-lung-cancer-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard
- License
- CC BY 4.0
- Published
- Jul 17, 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