Visium
Human stomach
GSM6177609
bronze Interactive viewer H&E gastrointestinal stromal tumor Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6177609_NYU_GIST2_Vis_processed_hires_image': DataArray[cyx] (3, 1940, 2000)
│ └── 'GSM6177609_NYU_GIST2_Vis_processed_lowres_image': DataArray[cyx] (3, 582, 600)
├── Shapes
│ └── 'GSM6177609_NYU_GIST2_Vis_processed': GeoDataFrame shape: (2493, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2493, 33538)
with coordinate systems:
▸ 'GSM6177609_NYU_GIST2_Vis_processed', with elements:
GSM6177609_NYU_GIST2_Vis_processed_hires_image (Images), GSM6177609_NYU_GIST2_Vis_processed_lowres_image (Images), GSM6177609_NYU_GIST2_Vis_processed (Shapes)
▸ 'GSM6177609_NYU_GIST2_Vis_processed_downscaled_hires', with elements:
GSM6177609_NYU_GIST2_Vis_processed_hires_image (Images), GSM6177609_NYU_GIST2_Vis_processed (Shapes)
▸ 'GSM6177609_NYU_GIST2_Vis_processed_downscaled_lowres', with elements:
GSM6177609_NYU_GIST2_Vis_processed_lowres_image (Images), GSM6177609_NYU_GIST2_Vis_processed (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("5RZuAhiNSPyEVscw") # 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/5RZuAhiNSPyEVscw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5RZuAhiNSPyEVscw Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["5RZuAhiNSPyEVscw0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment→ 12 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- stomach
- Condition
- gastrointestinal stromal tumor
- Modality
- RNA
- Observations
- 2,493
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,940 px
- mpp
- 3.521 µm/px
- Size
- 25 MB
- Sample ID
- GSM6177609
- License
- unknown
- Published
- Aug 5, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB