Visium
Human craniocervical region
GSM5494481
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5494481_P210325T5_hires_image': DataArray[cyx] (3, 2000, 1946)
├── Shapes
│ └── 'GSM5494481_P210325T5': GeoDataFrame shape: (1470, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1470, 36601)
with coordinate systems:
▸ 'GSM5494481_P210325T5', with elements:
GSM5494481_P210325T5_hires_image (Images), GSM5494481_P210325T5 (Shapes)
▸ 'GSM5494481_P210325T5_downscaled_hires', with elements:
GSM5494481_P210325T5_hires_image (Images), GSM5494481_P210325T5 (Shapes)
▸ 'GSM5494481_P210325T5_downscaled_lowres', with elements:
GSM5494481_P210325T5 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("PfZFVHZCbSWmBpjY") # 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/PfZFVHZCbSWmBpjY
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PfZFVHZCbSWmBpjY Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["PfZFVHZCbSWmBpjY0000"])[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
- 1,470
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,946 × 2,000 px
- mpp
- 3.885 µm/px
- Size
- 12 MB
- Sample ID
- GSM5494481
- 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