Visium
Human lymph node
GSM5732359
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5732359_C_hires_image': DataArray[cyx] (3, 2000, 1984)
├── Shapes
│ └── 'GSM5732359_C': GeoDataFrame shape: (4988, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4988, 33931)
with coordinate systems:
▸ 'GSM5732359_C', with elements:
GSM5732359_C_hires_image (Images), GSM5732359_C (Shapes)
▸ 'GSM5732359_C_downscaled_hires', with elements:
GSM5732359_C_hires_image (Images), GSM5732359_C (Shapes)
▸ 'GSM5732359_C_downscaled_lowres', with elements:
GSM5732359_C (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("yTFFOKDVp0vTvXw1") # 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/yTFFOKDVp0vTvXw1
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yTFFOKDVp0vTvXw1 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["yTFFOKDVp0vTvXw10000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients (10x Visium)→ 4 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymph node
- Condition
- breast cancer
- Modality
- RNA
- Observations
- 4,988
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,984 × 2,000 px
- mpp
- 3.505 µm/px
- Size
- 107 MB
- Sample ID
- GSM5732359
- License
- unknown
- Published
- Apr 30, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB