Visium
Mouse lung
GSM6634338
bronze Interactive viewer H&E lung adenocarcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6634338_Ctrl2_D1_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM6634338_Ctrl2_D1_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM6634338_Ctrl2_D1': GeoDataFrame shape: (2937, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2937, 30970)
with coordinate systems:
▸ 'GSM6634338_Ctrl2_D1', with elements:
GSM6634338_Ctrl2_D1_hires_image (Images), GSM6634338_Ctrl2_D1_lowres_image (Images), GSM6634338_Ctrl2_D1 (Shapes)
▸ 'GSM6634338_Ctrl2_D1_downscaled_hires', with elements:
GSM6634338_Ctrl2_D1_hires_image (Images), GSM6634338_Ctrl2_D1 (Shapes)
▸ 'GSM6634338_Ctrl2_D1_downscaled_lowres', with elements:
GSM6634338_Ctrl2_D1_lowres_image (Images), GSM6634338_Ctrl2_D1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("UZ9wYFtJ4M7KYRpA") # 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/UZ9wYFtJ4M7KYRpA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UZ9wYFtJ4M7KYRpA Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["UZ9wYFtJ4M7KYRpA0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies [visium]→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Condition
- lung adenocarcinoma
- Modality
- RNA
- Observations
- 2,937
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.729 µm/px
- Size
- 39 MB
- Sample ID
- GSM6634338
- License
- unknown
- Published
- May 3, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB