Visium
Human lung
GSM8699173
bronze Interactive viewer H&E obsolete idiopathic pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8699173_JKPF3_5_hires_image': DataArray[cyx] (3, 2000, 1818)
│ └── 'GSM8699173_JKPF3_5_lowres_image': DataArray[cyx] (4, 600, 546)
├── Shapes
│ └── 'GSM8699173_JKPF3_5': GeoDataFrame shape: (2130, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2130, 33538)
with coordinate systems:
▸ 'GSM8699173_JKPF3_5', with elements:
GSM8699173_JKPF3_5_hires_image (Images), GSM8699173_JKPF3_5_lowres_image (Images), GSM8699173_JKPF3_5 (Shapes)
▸ 'GSM8699173_JKPF3_5_downscaled_hires', with elements:
GSM8699173_JKPF3_5_hires_image (Images), GSM8699173_JKPF3_5 (Shapes)
▸ 'GSM8699173_JKPF3_5_downscaled_lowres', with elements:
GSM8699173_JKPF3_5_lowres_image (Images), GSM8699173_JKPF3_5 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("kzKq7dJCHTJi3WWw") # 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/kzKq7dJCHTJi3WWw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kzKq7dJCHTJi3WWw Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["kzKq7dJCHTJi3WWw0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatially resolved atlas of IPF fibroblastic foci identifies that PAK2 kinase activation is involved in fibrogenesis→ 9 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lung
- Condition
- obsolete idiopathic pulmonary fibrosis
- Modality
- RNA
- Observations
- 2,130
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,818 × 2,000 px
- mpp
- 4.050 µm/px
- Size
- 23 MB
- Sample ID
- GSM8699173
- License
- unknown
- Published
- Aug 11, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB