Visium
Mouse quadriceps femoris
GSM5979972
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5979972_C57BL10_hires_image': DataArray[cyx] (3, 2000, 1969)
│ └── 'GSM5979972_C57BL10_lowres_image': DataArray[cyx] (3, 600, 591)
├── Shapes
│ └── 'GSM5979972_C57BL10': GeoDataFrame shape: (2348, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2348, 32285)
with coordinate systems:
▸ 'GSM5979972_C57BL10', with elements:
GSM5979972_C57BL10_hires_image (Images), GSM5979972_C57BL10_lowres_image (Images), GSM5979972_C57BL10 (Shapes)
▸ 'GSM5979972_C57BL10_downscaled_hires', with elements:
GSM5979972_C57BL10_hires_image (Images), GSM5979972_C57BL10 (Shapes)
▸ 'GSM5979972_C57BL10_downscaled_lowres', with elements:
GSM5979972_C57BL10_lowres_image (Images), GSM5979972_C57BL10 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("xnILMMQJqj2SaDKC0000")
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("xnILMMQJqj2SaDKC") # 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 xnILMMQJqj2SaDKC0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/xnILMMQJqj2SaDKC
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xnILMMQJqj2SaDKCLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics (Visium, 10x Genomics) data of Duchenne mouse models→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- quadriceps femoris
- Modality
- RNA
- Observations (spots)
- 2,348
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,969 × 2,000 px
- mpp
- 3.684 µm/px
- Size
- 14.8 MB
- Sample ID
- GSM5979972
- License
- NCBI GEO policy
- Published
- Jun 28, 2023
Cite this dataset
doi.org/10.1038/s41467-023-40555-9 ↗ BibTeX
@article{Heezen_2023,
title = {Spatial transcriptomics reveal markers of histopathological changes in Duchenne muscular dystrophy mouse models},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-40555-9},
DOI = {10.1038/s41467-023-40555-9},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Heezen, L.G.M. and Abdelaal, T. and van Putten, M. and Aartsma-Rus, A. and Mahfouz, A. and Spitali, P.},
year = {2023},
month = Aug
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB