Visium
Human breast
GSM6433587
bronze Interactive viewer H&E triple-negative breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM6433587_093A_hires_image': DataArray[cyx] (3, 2000, 1969)
├── Shapes
│ └── 'GSM6433587_093A': GeoDataFrame shape: (1654, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1654, 36601)
with coordinate systems:
▸ 'GSM6433587_093A', with elements:
GSM6433587_093A_hires_image (Images), GSM6433587_093A (Shapes)
▸ 'GSM6433587_093A_downscaled_hires', with elements:
GSM6433587_093A_hires_image (Images), GSM6433587_093A (Shapes)
▸ 'GSM6433587_093A_downscaled_lowres', with elements:
GSM6433587_093A (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("x1116XWF9jKxf2ss") # 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/x1116XWF9jKxf2ss
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid x1116XWF9jKxf2ss Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["x1116XWF9jKxf2ss0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- triple-negative breast carcinoma
- Modality
- RNA
- Observations
- 1,654
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,969 × 2,000 px
- mpp
- 3.847 µm/px
- Size
- 31 MB
- Sample ID
- GSM6433587
- License
- unknown
- Published
- Nov 2, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB