Visium
Human breast
GSM7688224
bronze Interactive viewer H&E breast cancer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7688224_Tumor-897_hires_image': DataArray[cyx] (3, 1961, 2000)
│ └── 'GSM7688224_Tumor-897_lowres_image': DataArray[cyx] (3, 589, 600)
├── Shapes
│ └── 'GSM7688224_Tumor-897': GeoDataFrame shape: (2536, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2536, 36601)
with coordinate systems:
▸ 'GSM7688224_Tumor-897', with elements:
GSM7688224_Tumor-897_hires_image (Images), GSM7688224_Tumor-897_lowres_image (Images), GSM7688224_Tumor-897 (Shapes)
▸ 'GSM7688224_Tumor-897_downscaled_hires', with elements:
GSM7688224_Tumor-897_hires_image (Images), GSM7688224_Tumor-897 (Shapes)
▸ 'GSM7688224_Tumor-897_downscaled_lowres', with elements:
GSM7688224_Tumor-897_lowres_image (Images), GSM7688224_Tumor-897 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("1yTtZCYrcefxMlNm") # 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/1yTtZCYrcefxMlNm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1yTtZCYrcefxMlNm Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["1yTtZCYrcefxMlNm0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial Transcriptomics reveals that cells that experience intratumoral hypoxia retain hypoxia-associated transcriptional programs after invading into oxygenated tumor regions.→ 2 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations
- 2,536
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,961 px
- mpp
- 3.415 µm/px
- Size
- 46 MB
- Sample ID
- GSM7688224
- License
- unknown
- Published
- Jul 2, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB