Visium
Mouse lung
GSM8428411
bronze Interactive viewer H&E breast cancer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8428411_09.9_628_LUNG_V11Y03-083_D_hires_image': DataArray[cyx] (3, 1256, 2000)
│ └── 'GSM8428411_09.9_628_LUNG_V11Y03-083_D_lowres_image': DataArray[cyx] (3, 377, 600)
├── Shapes
│ └── 'GSM8428411_09.9_628_LUNG_V11Y03-083_D': GeoDataFrame shape: (2780, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2780, 19465)
with coordinate systems:
▸ 'GSM8428411_09.9_628_LUNG_V11Y03-083_D', with elements:
GSM8428411_09.9_628_LUNG_V11Y03-083_D_hires_image (Images), GSM8428411_09.9_628_LUNG_V11Y03-083_D_lowres_image (Images), GSM8428411_09.9_628_LUNG_V11Y03-083_D (Shapes)
▸ 'GSM8428411_09.9_628_LUNG_V11Y03-083_D_downscaled_hires', with elements:
GSM8428411_09.9_628_LUNG_V11Y03-083_D_hires_image (Images), GSM8428411_09.9_628_LUNG_V11Y03-083_D (Shapes)
▸ 'GSM8428411_09.9_628_LUNG_V11Y03-083_D_downscaled_lowres', with elements:
GSM8428411_09.9_628_LUNG_V11Y03-083_D_lowres_image (Images), GSM8428411_09.9_628_LUNG_V11Y03-083_D (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("nUXKOIM4VVswEGtd") # 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/nUXKOIM4VVswEGtd
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid nUXKOIM4VVswEGtd Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["nUXKOIM4VVswEGtd0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Extraction of a Stromal Metastatic Gene Signature in Breast Cancer via Spatial Profiling→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Condition
- breast cancer
- Modality
- RNA
- Observations
- 2,780
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,256 px
- mpp
- 5.432 µm/px
- Size
- 41 MB
- Sample ID
- GSM8428411
- License
- unknown
- Published
- Aug 4, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB