Visium
Human breast
GSM6592052
bronze Interactive viewer H&E triple-negative breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM6592052_M5_hires_image': DataArray[cyx] (3, 1989, 2000)
├── Shapes
│ └── 'GSM6592052_M5': GeoDataFrame shape: (2104, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2104, 36601)
with coordinate systems:
▸ 'GSM6592052_M5', with elements:
GSM6592052_M5_hires_image (Images), GSM6592052_M5 (Shapes)
▸ 'GSM6592052_M5_downscaled_hires', with elements:
GSM6592052_M5_hires_image (Images), GSM6592052_M5 (Shapes)
▸ 'GSM6592052_M5_downscaled_lowres', with elements:
GSM6592052_M5 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("b3XMORLWT3g06eNt") # 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/b3XMORLWT3g06eNt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid b3XMORLWT3g06eNt Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["b3XMORLWT3g06eNt0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomics of human plastic and non-plastic breast cancer subtypes→ 14 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- triple-negative breast carcinoma
- Modality
- RNA
- Observations
- 2,104
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,989 px
- mpp
- 3.419 µm/px
- Size
- 25 MB
- Sample ID
- GSM6592052
- License
- unknown
- Published
- Oct 16, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB