Visium
Mouse lung
GSM7978619
bronze Interactive viewer H&E pulmonary fibrosis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7978619_B1_hires_image': DataArray[cyx] (3, 2000, 1817)
│ └── 'GSM7978619_B1_lowres_image': DataArray[cyx] (3, 600, 545)
├── Shapes
│ └── 'GSM7978619_B1': GeoDataFrame shape: (2775, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2775, 32285)
with coordinate systems:
▸ 'GSM7978619_B1', with elements:
GSM7978619_B1_hires_image (Images), GSM7978619_B1_lowres_image (Images), GSM7978619_B1 (Shapes)
▸ 'GSM7978619_B1_downscaled_hires', with elements:
GSM7978619_B1_hires_image (Images), GSM7978619_B1 (Shapes)
▸ 'GSM7978619_B1_downscaled_lowres', with elements:
GSM7978619_B1_lowres_image (Images), GSM7978619_B1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("3JTVLlyZPSZ436Qr") # 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/3JTVLlyZPSZ436Qr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3JTVLlyZPSZ436Qr Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3JTVLlyZPSZ436Qr0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Histological Signatures Reveal Anti-Fibrotic Factors in Mouse and Human Lungs [Visium]→ 8 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Condition
- pulmonary fibrosis
- Modality
- RNA
- Observations
- 2,775
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,817 × 2,000 px
- mpp
- 4.049 µm/px
- Size
- 12 MB
- Sample ID
- GSM7978619
- License
- unknown
- Published
- Jan 7, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB