Visium
Human kidney
GSM7115964
silver Interactive viewer H&E acute kidney failure No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7115964_D15_hires_image': DataArray[cyx] (3, 1938, 2000)
│ └── 'GSM7115964_D15_lowres_image': DataArray[cyx] (3, 582, 600)
├── Shapes
│ └── 'GSM7115964_D15': GeoDataFrame shape: (3794, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3794, 36601)
with coordinate systems:
▸ 'GSM7115964_D15', with elements:
GSM7115964_D15_hires_image (Images), GSM7115964_D15_lowres_image (Images), GSM7115964_D15 (Shapes)
▸ 'GSM7115964_D15_downscaled_hires', with elements:
GSM7115964_D15_hires_image (Images), GSM7115964_D15 (Shapes)
▸ 'GSM7115964_D15_downscaled_lowres', with elements:
GSM7115964_D15_lowres_image (Images), GSM7115964_D15 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("pkMzcQE2yT1H0l290000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("pkMzcQE2yT1H0l29") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download pkMzcQE2yT1H0l290000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pkMzcQE2yT1H0l29
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pkMzcQE2yT1H0l29License: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Condition
- acute kidney failure
- Modality
- RNA
- Observations (spots)
- 3,794
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,938 px
- mpp
- 3.676 µm/px
- Size
- 25.6 MB
- Sample ID
- GSM7115964
- License
- NCBI GEO policy
- Published
- Mar 31, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB