Visium
Human lung
GSM8087038
bronze Interactive viewer H&E obsolete idiopathic pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8087038_IPF12_hires_image': DataArray[cyx] (3, 1981, 2000)
│ └── 'GSM8087038_IPF12_lowres_image': DataArray[cyx] (3, 595, 600)
├── Shapes
│ └── 'GSM8087038_IPF12': GeoDataFrame shape: (2753, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2753, 36601)
with coordinate systems:
▸ 'GSM8087038_IPF12', with elements:
GSM8087038_IPF12_hires_image (Images), GSM8087038_IPF12_lowres_image (Images), GSM8087038_IPF12 (Shapes)
▸ 'GSM8087038_IPF12_downscaled_hires', with elements:
GSM8087038_IPF12_hires_image (Images), GSM8087038_IPF12 (Shapes)
▸ 'GSM8087038_IPF12_downscaled_lowres', with elements:
GSM8087038_IPF12_lowres_image (Images), GSM8087038_IPF12 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("PgLUcgUYCMc4TwWg") # 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/PgLUcgUYCMc4TwWg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid PgLUcgUYCMc4TwWg Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["PgLUcgUYCMc4TwWg0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial deconvolution of tertiary lymphoid structure in human IPF lungs revealed novel CCL19-expressing mural cells→ 14 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lung
- Condition
- obsolete idiopathic pulmonary fibrosis
- Modality
- RNA
- Observations
- 2,753
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,981 px
- mpp
- 3.485 µm/px
- Size
- 16 MB
- Sample ID
- GSM8087038
- License
- unknown
- Published
- Nov 22, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB