Visium
Mouse brain
GSM5519055
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5519055_hemeHpx_1000_hires_image': DataArray[cyx] (3, 2000, 1771)
│ └── 'GSM5519055_hemeHpx_1000_lowres_image': DataArray[cyx] (3, 600, 531)
├── Shapes
│ └── 'GSM5519055_hemeHpx_1000': GeoDataFrame shape: (2936, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2936, 26124)
with coordinate systems:
▸ 'GSM5519055_hemeHpx_1000', with elements:
GSM5519055_hemeHpx_1000_hires_image (Images), GSM5519055_hemeHpx_1000_lowres_image (Images), GSM5519055_hemeHpx_1000 (Shapes)
▸ 'GSM5519055_hemeHpx_1000_downscaled_hires', with elements:
GSM5519055_hemeHpx_1000_hires_image (Images), GSM5519055_hemeHpx_1000 (Shapes)
▸ 'GSM5519055_hemeHpx_1000_downscaled_lowres', with elements:
GSM5519055_hemeHpx_1000_lowres_image (Images), GSM5519055_hemeHpx_1000 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("4N1mcnugE77SMwNo0000")
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("4N1mcnugE77SMwNo") # 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 4N1mcnugE77SMwNo0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/4N1mcnugE77SMwNo
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 4N1mcnugE77SMwNoLicense: NCBI GEO policy
Part of collection
Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain→ 7 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,936
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,771 × 2,000 px
- mpp
- 4.219 µm/px
- Size
- 43.8 MB
- Sample ID
- GSM5519055
- License
- NCBI GEO policy
- Published
- Nov 25, 2021
Cite this dataset
doi.org/10.1016/j.freeradbiomed.2021.11.011 ↗ BibTeX
@article{Buzzi_2022,
title = {Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain},
volume = {179},
ISSN = {0891-5849},
url = {http://dx.doi.org/10.1016/j.freeradbiomed.2021.11.011},
DOI = {10.1016/j.freeradbiomed.2021.11.011},
journal = {Free Radical Biology and Medicine},
publisher = {Elsevier BV},
author = {Buzzi, Raphael M. and Akeret, Kevin and Schwendinger, Nina and Klohs, Jan and Vallelian, Florence and Hugelshofer, Michael and Schaer, Dominik J.},
year = {2022},
month = Feb,
pages = {277–287}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB