Visium
Human craniocervical region
GSM5494476
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5494476_HNSCC201125T05_hires_image': DataArray[cyx] (3, 1946, 2000)
├── Shapes
│ └── 'GSM5494476_HNSCC201125T05': GeoDataFrame shape: (1726, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1726, 36601)
with coordinate systems:
▸ 'GSM5494476_HNSCC201125T05', with elements:
GSM5494476_HNSCC201125T05_hires_image (Images), GSM5494476_HNSCC201125T05 (Shapes)
▸ 'GSM5494476_HNSCC201125T05_downscaled_hires', with elements:
GSM5494476_HNSCC201125T05_hires_image (Images), GSM5494476_HNSCC201125T05 (Shapes)
▸ 'GSM5494476_HNSCC201125T05_downscaled_lowres', with elements:
GSM5494476_HNSCC201125T05 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("KDzTowEVFnswH79O") # 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/KDzTowEVFnswH79O
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid KDzTowEVFnswH79O Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["KDzTowEVFnswH79O0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Visium Analysis of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- craniocervical region
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 1,726
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,946 px
- mpp
- 3.406 µm/px
- Size
- 20 MB
- Sample ID
- GSM5494476
- License
- unknown
- Published
- Aug 29, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB