Visium
Human lymph node
GSM5732360
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5732360_D_hires_image': DataArray[cyx] (3, 1969, 2000)
├── Shapes
│ └── 'GSM5732360_D': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 33931)
with coordinate systems:
▸ 'GSM5732360_D', with elements:
GSM5732360_D_hires_image (Images), GSM5732360_D (Shapes)
▸ 'GSM5732360_D_downscaled_hires', with elements:
GSM5732360_D_hires_image (Images), GSM5732360_D (Shapes)
▸ 'GSM5732360_D_downscaled_lowres', with elements:
GSM5732360_D (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("HXcV5nl6VH6xpKft0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("HXcV5nl6VH6xpKft") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download HXcV5nl6VH6xpKft0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/HXcV5nl6VH6xpKft
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid HXcV5nl6VH6xpKftLicense: NCBI GEO policy
Part 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 (spots)
- 4,992
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,969 px
- mpp
- 3.524 µm/px
- Size
- 107 MB
- Sample ID
- GSM5732360
- License
- NCBI GEO policy
- Published
- Apr 30, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB