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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("PgLUcgUYCMc4TwWg0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("PgLUcgUYCMc4TwWg") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download PgLUcgUYCMc4TwWg0000 --dest data/
# or lamin: 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 PgLUcgUYCMc4TwWgLicense: NCBI GEO policy
Part 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 (spots)
- 2,753
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,981 px
- mpp
- 3.485 µm/px
- Size
- 16.4 MB
- Sample ID
- GSM8087038
- License
- NCBI GEO policy
- Published
- Nov 22, 2024
Cite this dataset
doi.org/10.1183/13993003.01114-2024 ↗ BibTeX
@article{Yang_2025,
title = {Distinct mural cells and fibroblasts promote pathogenic plasma cell accumulation in idiopathic pulmonary fibrosis},
volume = {65},
ISSN = {1399-3003},
url = {http://dx.doi.org/10.1183/13993003.01114-2024},
DOI = {10.1183/13993003.01114-2024},
number = {6},
journal = {European Respiratory Journal},
publisher = {European Respiratory Society (ERS)},
author = {Yang, Zhi and Cao, Gaoyuan and Tan, Xiaosheng and Orfanos, Sarah and Jude, Joseph and Barbet, Gaetan and An, Steven S. and Jiang, Dianhua and Panettieri, Reynold A. and Yang, Qi},
year = {2025},
month = Feb,
pages = {2401114}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB