Visium
Rat brainstem
GSM8125596
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8125596_5_S5_hires_image': DataArray[cyx] (3, 1922, 2000)
│ └── 'GSM8125596_5_S5_lowres_image': DataArray[cyx] (3, 577, 600)
├── Shapes
│ └── 'GSM8125596_5_S5': GeoDataFrame shape: (2182, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2182, 25340)
with coordinate systems:
▸ 'GSM8125596_5_S5', with elements:
GSM8125596_5_S5_hires_image (Images), GSM8125596_5_S5_lowres_image (Images), GSM8125596_5_S5 (Shapes)
▸ 'GSM8125596_5_S5_downscaled_hires', with elements:
GSM8125596_5_S5_hires_image (Images), GSM8125596_5_S5 (Shapes)
▸ 'GSM8125596_5_S5_downscaled_lowres', with elements:
GSM8125596_5_S5_lowres_image (Images), GSM8125596_5_S5 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ZqJEYNxHBSymjQ1s0000")
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("ZqJEYNxHBSymjQ1s") # 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 ZqJEYNxHBSymjQ1s0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZqJEYNxHBSymjQ1s
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZqJEYNxHBSymjQ1sLicense: NCBI GEO policy
Part of collection
Neuromodulatory co-expression in cardiac vagal motor neurons of the Dorsal Motor Nucleus of the Vagus [spatial transcriptomics]→ 8 datasets · other
Metadata
- Technology
- Visium
- Organism
- rat
- Tissue
- brainstem
- Modality
- RNA
- Observations (spots)
- 2,182
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,922 px
- mpp
- 3.547 µm/px
- Size
- 20.0 MB
- Sample ID
- GSM8125596
- License
- NCBI GEO policy
- Published
- Jul 22, 2024
Cite this dataset
doi.org/10.1016/j.isci.2024.110549 ↗ BibTeX
@article{Hornung_2024,
title = {Neuromodulatory co-expression in cardiac vagal motor neurons of the dorsal motor nucleus of the vagus},
volume = {27},
ISSN = {2589-0042},
url = {http://dx.doi.org/10.1016/j.isci.2024.110549},
DOI = {10.1016/j.isci.2024.110549},
number = {8},
journal = {iScience},
publisher = {Elsevier BV},
author = {Hornung, Eden and Robbins, Shaina and Srivastava, Ankita and Achanta, Sirisha and Chen, Jin and Cheng, Zixi Jack and Schwaber, James and Vadigepalli, Rajanikanth},
year = {2024},
month = Aug,
pages = {110549}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB