Visium
Human liver
GSM8569296
bronze H&E COVID-19 Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8569296_Moderate_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM8569296_Moderate_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM8569296_Moderate': GeoDataFrame shape: (4778, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4778, 37082)
with coordinate systems:
▸ 'GSM8569296_Moderate', with elements:
GSM8569296_Moderate_hires_image (Images), GSM8569296_Moderate_lowres_image (Images), GSM8569296_Moderate (Shapes)
▸ 'GSM8569296_Moderate_downscaled_hires', with elements:
GSM8569296_Moderate_hires_image (Images), GSM8569296_Moderate (Shapes)
▸ 'GSM8569296_Moderate_downscaled_lowres', with elements:
GSM8569296_Moderate_lowres_image (Images), GSM8569296_Moderate (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("rF35Rfn5wp76F96x") # 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/rF35Rfn5wp76F96x
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rF35Rfn5wp76F96x Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["rF35Rfn5wp76F96x0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomical analysis of livers from patients with COVID19→ 3 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- liver
- Condition
- COVID-19
- Modality
- RNA
- Observations
- 4,778
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 2,000 px
- mpp
- 5.442 µm/px
- Size
- 12 MB
- Sample ID
- GSM8569296
- License
- unknown
- Published
- Oct 25, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB