Visium
Mouse descending colon
GSM7508785
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7508785_V10S15-056_D_hires_image': DataArray[cyx] (3, 1807, 2000)
│ └── 'GSM7508785_V10S15-056_D_lowres_image': DataArray[cyx] (3, 542, 600)
├── Shapes
│ └── 'GSM7508785_V10S15-056_D': GeoDataFrame shape: (572, 2) (2D shapes)
└── Tables
└── 'table': AnnData (572, 32285)
with coordinate systems:
▸ 'GSM7508785_V10S15-056_D', with elements:
GSM7508785_V10S15-056_D_hires_image (Images), GSM7508785_V10S15-056_D_lowres_image (Images), GSM7508785_V10S15-056_D (Shapes)
▸ 'GSM7508785_V10S15-056_D_downscaled_hires', with elements:
GSM7508785_V10S15-056_D_hires_image (Images), GSM7508785_V10S15-056_D (Shapes)
▸ 'GSM7508785_V10S15-056_D_downscaled_lowres', with elements:
GSM7508785_V10S15-056_D_lowres_image (Images), GSM7508785_V10S15-056_D (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("xKKNBxElQ4QjXFWg") # 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/xKKNBxElQ4QjXFWg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xKKNBxElQ4QjXFWg Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["xKKNBxElQ4QjXFWg0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial Transcriptomic profiling of day2 wounds and intact tissues of Hgfac WT and KO mice→ 3 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- descending colon
- Modality
- RNA
- Observations
- 572
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,807 px
- mpp
- 4.641 µm/px
- Size
- 11 MB
- Sample ID
- GSM7508785
- License
- unknown
- Published
- Oct 26, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB