Visium
Human kidney
GSM7974478
bronze Interactive viewer H&E pauci-immune glomerulonephritis with ANCA Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7974478_V5_A_hires_image': DataArray[cyx] (3, 2000, 1949)
│ └── 'GSM7974478_V5_A_lowres_image': DataArray[cyx] (3, 600, 585)
├── Shapes
│ └── 'GSM7974478_V5_A': GeoDataFrame shape: (624, 2) (2D shapes)
└── Tables
└── 'table': AnnData (624, 17943)
with coordinate systems:
▸ 'GSM7974478_V5_A', with elements:
GSM7974478_V5_A_hires_image (Images), GSM7974478_V5_A_lowres_image (Images), GSM7974478_V5_A (Shapes)
▸ 'GSM7974478_V5_A_downscaled_hires', with elements:
GSM7974478_V5_A_hires_image (Images), GSM7974478_V5_A (Shapes)
▸ 'GSM7974478_V5_A_downscaled_lowres', with elements:
GSM7974478_V5_A_lowres_image (Images), GSM7974478_V5_A (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("8vLh13yl5w6dZ5EZ") # 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/8vLh13yl5w6dZ5EZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8vLh13yl5w6dZ5EZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["8vLh13yl5w6dZ5EZ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Immune profiling-based targeting of pathogenic T cells with ustekinumab in ANCA-associated glomerulonephritis→ 23 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Condition
- pauci-immune glomerulonephritis with ANCA
- Modality
- RNA
- Observations
- 624
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,949 × 2,000 px
- mpp
- 3.576 µm/px
- Size
- 10 MB
- Sample ID
- GSM7974478
- License
- unknown
- Published
- Jun 28, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB