Visium
Human ovary
GSM6506112
silver Interactive viewer H&E ovarian serous adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6506112_SP3_hires_image': DataArray[cyx] (3, 2000, 1903)
│ └── 'GSM6506112_SP3_lowres_image': DataArray[cyx] (3, 600, 571)
├── Shapes
│ └── 'GSM6506112_SP3': GeoDataFrame shape: (1504, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1504, 33538)
with coordinate systems:
▸ 'GSM6506112_SP3', with elements:
GSM6506112_SP3_hires_image (Images), GSM6506112_SP3_lowres_image (Images), GSM6506112_SP3 (Shapes)
▸ 'GSM6506112_SP3_downscaled_hires', with elements:
GSM6506112_SP3_hires_image (Images), GSM6506112_SP3 (Shapes)
▸ 'GSM6506112_SP3_downscaled_lowres', with elements:
GSM6506112_SP3_lowres_image (Images), GSM6506112_SP3 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("1KOUlpST5EqHJdGZ") # 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/1KOUlpST5EqHJdGZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1KOUlpST5EqHJdGZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["1KOUlpST5EqHJdGZ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- ovary
- Condition
- ovarian serous adenocarcinoma
- Modality
- RNA
- Observations
- 1,504
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,903 × 2,000 px
- mpp
- 3.695 µm/px
- Size
- 21 MB
- Sample ID
- GSM6506112
- 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