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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("rq6uDW2TnzfTpQzd0000")
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("rq6uDW2TnzfTpQzd") # 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 rq6uDW2TnzfTpQzd0000 --dest data/
# or lamin: 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 rq6uDW2TnzfTpQzdLicense: NCBI GEO policy
Part 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 (spots)
- 2,769
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.624 µm/px
- Size
- 32.4 MB
- Sample ID
- GSM6585869
- License
- NCBI GEO policy
- 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 ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB