Visium
Human lymph node
GSM8633894
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8633894_21_01570_LI_SING_hires_image': DataArray[cyx] (3, 2000, 1985)
│ └── 'GSM8633894_21_01570_LI_SING_lowres_image': DataArray[cyx] (3, 600, 596)
├── Shapes
│ └── 'GSM8633894_21_01570_LI_SING': GeoDataFrame shape: (1908, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1908, 36601)
with coordinate systems:
▸ 'GSM8633894_21_01570_LI_SING', with elements:
GSM8633894_21_01570_LI_SING_hires_image (Images), GSM8633894_21_01570_LI_SING_lowres_image (Images), GSM8633894_21_01570_LI_SING (Shapes)
▸ 'GSM8633894_21_01570_LI_SING_downscaled_hires', with elements:
GSM8633894_21_01570_LI_SING_hires_image (Images), GSM8633894_21_01570_LI_SING (Shapes)
▸ 'GSM8633894_21_01570_LI_SING_downscaled_lowres', with elements:
GSM8633894_21_01570_LI_SING_lowres_image (Images), GSM8633894_21_01570_LI_SING (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("aHg75Ot5HyjdkY6o") # 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/aHg75Ot5HyjdkY6o
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid aHg75Ot5HyjdkY6o Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["aHg75Ot5HyjdkY6o0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences→ 5 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymph node
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations
- 1,908
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,985 × 2,000 px
- mpp
- 3.270 µm/px
- Size
- 23 MB
- Sample ID
- GSM8633894
- License
- unknown
- Published
- Nov 20, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB