Visium
Mouse lung
GSM6585869
bronze Interactive viewer H&E influenza Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6585869_R3_Spatial_31dpi_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM6585869_R3_Spatial_31dpi_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM6585869_R3_Spatial_31dpi': GeoDataFrame shape: (2769, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2769, 32285)
with coordinate systems:
▸ 'GSM6585869_R3_Spatial_31dpi', with elements:
GSM6585869_R3_Spatial_31dpi_hires_image (Images), GSM6585869_R3_Spatial_31dpi_lowres_image (Images), GSM6585869_R3_Spatial_31dpi (Shapes)
▸ 'GSM6585869_R3_Spatial_31dpi_downscaled_hires', with elements:
GSM6585869_R3_Spatial_31dpi_hires_image (Images), GSM6585869_R3_Spatial_31dpi (Shapes)
▸ 'GSM6585869_R3_Spatial_31dpi_downscaled_lowres', with elements:
GSM6585869_R3_Spatial_31dpi_lowres_image (Images), GSM6585869_R3_Spatial_31dpi (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("rq6uDW2TnzfTpQzd") # 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/rq6uDW2TnzfTpQzd
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rq6uDW2TnzfTpQzd Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["rq6uDW2TnzfTpQzd0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection.→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Condition
- influenza
- Modality
- RNA
- Observations
- 2,769
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.624 µm/px
- Size
- 31 MB
- Sample ID
- GSM6585869
- License
- unknown
- Published
- Aug 8, 2023
Cite this dataset
doi.org/10.1038/s41467-023-41387-3 ↗ BibTeX
@article{Beppu_2023,
title = {Epithelial plasticity and innate immune activation promote lung tissue remodeling following respiratory viral infection},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-41387-3},
DOI = {10.1038/s41467-023-41387-3},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Beppu, Andrew K. and Zhao, Juanjuan and Yao, Changfu and Carraro, Gianni and Israely, Edo and Coelho, Anna Lucia and Drake, Katherine and Hogaboam, Cory M. and Parks, William C. and Kolls, Jay K. and Stripp, Barry R.},
year = {2023},
month = Sept
}Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB