Visium
Mouse liver
GSM8404656
silver Interactive viewer H&E drug-induced liver injury No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8404656_APAP24h_hires_image': DataArray[cyx] (3, 2000, 1957)
│ └── 'GSM8404656_APAP24h_lowres_image': DataArray[cyx] (3, 600, 587)
├── Shapes
│ └── 'GSM8404656_APAP24h': GeoDataFrame shape: (1655, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1655, 32285)
with coordinate systems:
▸ 'GSM8404656_APAP24h', with elements:
GSM8404656_APAP24h_hires_image (Images), GSM8404656_APAP24h_lowres_image (Images), GSM8404656_APAP24h (Shapes)
▸ 'GSM8404656_APAP24h_downscaled_hires', with elements:
GSM8404656_APAP24h_hires_image (Images), GSM8404656_APAP24h (Shapes)
▸ 'GSM8404656_APAP24h_downscaled_lowres', with elements:
GSM8404656_APAP24h_lowres_image (Images), GSM8404656_APAP24h (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("1i7fm72J5YDINUZz") # 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/1i7fm72J5YDINUZz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1i7fm72J5YDINUZz Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["1i7fm72J5YDINUZz0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury (10x Visium)→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- liver
- Condition
- drug-induced liver injury
- Modality
- RNA
- Observations
- 1,655
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,957 × 2,000 px
- mpp
- 3.411 µm/px
- Size
- 25 MB
- Sample ID
- GSM8404656
- License
- unknown
- Published
- Sep 17, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB