Visium
Mouse intestine
GSM7840111
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7840111_V11Y11-297_C_hires_image': DataArray[cyx] (3, 1613, 2000)
│ └── 'GSM7840111_V11Y11-297_C_lowres_image': DataArray[cyx] (3, 484, 600)
├── Shapes
│ └── 'GSM7840111_V11Y11-297_C': GeoDataFrame shape: (2761, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2761, 32285)
with coordinate systems:
▸ 'GSM7840111_V11Y11-297_C', with elements:
GSM7840111_V11Y11-297_C_hires_image (Images), GSM7840111_V11Y11-297_C_lowres_image (Images), GSM7840111_V11Y11-297_C (Shapes)
▸ 'GSM7840111_V11Y11-297_C_downscaled_hires', with elements:
GSM7840111_V11Y11-297_C_hires_image (Images), GSM7840111_V11Y11-297_C (Shapes)
▸ 'GSM7840111_V11Y11-297_C_downscaled_lowres', with elements:
GSM7840111_V11Y11-297_C_lowres_image (Images), GSM7840111_V11Y11-297_C (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("8DnqstW5tS7TDcJQ") # 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/8DnqstW5tS7TDcJQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8DnqstW5tS7TDcJQ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["8DnqstW5tS7TDcJQ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]→ 45 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- intestine
- Modality
- RNA
- Observations
- 2,761
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,613 px
- mpp
- 4.639 µm/px
- Size
- 36 MB
- Sample ID
- GSM7840111
- License
- unknown
- Published
- Nov 26, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB