Visium
Rat brainstem
GSM8125599
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8125599_8_S8_hires_image': DataArray[cyx] (3, 1826, 2000)
│ └── 'GSM8125599_8_S8_lowres_image': DataArray[cyx] (3, 548, 600)
├── Shapes
│ └── 'GSM8125599_8_S8': GeoDataFrame shape: (2199, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2199, 25340)
with coordinate systems:
▸ 'GSM8125599_8_S8', with elements:
GSM8125599_8_S8_hires_image (Images), GSM8125599_8_S8_lowres_image (Images), GSM8125599_8_S8 (Shapes)
▸ 'GSM8125599_8_S8_downscaled_hires', with elements:
GSM8125599_8_S8_hires_image (Images), GSM8125599_8_S8 (Shapes)
▸ 'GSM8125599_8_S8_downscaled_lowres', with elements:
GSM8125599_8_S8_lowres_image (Images), GSM8125599_8_S8 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("v5GSGsfCbHqiN0WZ") # 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/v5GSGsfCbHqiN0WZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid v5GSGsfCbHqiN0WZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["v5GSGsfCbHqiN0WZ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 2,199
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,826 px
- mpp
- 3.680 µm/px
- Size
- 18 MB
- Sample ID
- GSM8125599
- License
- unknown
- Published
- Jul 22, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB