Visium
Human breast
GSM7777522
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7777522_C1_hires_image': DataArray[cyx] (3, 1819, 2000)
│ └── 'GSM7777522_C1_lowres_image': DataArray[cyx] (3, 546, 600)
├── Shapes
│ └── 'GSM7777522_C1': GeoDataFrame shape: (642, 2) (2D shapes)
└── Tables
└── 'table': AnnData (642, 36601)
with coordinate systems:
▸ 'GSM7777522_C1', with elements:
GSM7777522_C1_hires_image (Images), GSM7777522_C1_lowres_image (Images), GSM7777522_C1 (Shapes)
▸ 'GSM7777522_C1_downscaled_hires', with elements:
GSM7777522_C1_hires_image (Images), GSM7777522_C1 (Shapes)
▸ 'GSM7777522_C1_downscaled_lowres', with elements:
GSM7777522_C1_lowres_image (Images), GSM7777522_C1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("AhpyOhNEqr6qyka5") # 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/AhpyOhNEqr6qyka5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AhpyOhNEqr6qyka5 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["AhpyOhNEqr6qyka50000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Cancer-associated Fibroblast Spatial Heterogeneity and EMILIN1 Expression in Cancer Stroma Modulate TGF-b Activity and CD8+ T-Cell Infiltration in Breast Cancer→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations
- 642
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,819 px
- mpp
- 4.050 µm/px
- Size
- 13 MB
- Sample ID
- GSM7777522
- License
- unknown
- Published
- Apr 16, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB