Visium
Mouse kidney
GSM7090416
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7090416_visium_sham_male_spaceranger_outs_hires_image': DataArray[cyx] (3, 1938, 2000)
│ └── 'GSM7090416_visium_sham_male_spaceranger_outs_lowres_image': DataArray[cyx] (3, 582, 600)
├── Shapes
│ └── 'GSM7090416_visium_sham_male_spaceranger_outs': GeoDataFrame shape: (1815, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1815, 32285)
with coordinate systems:
▸ 'GSM7090416_visium_sham_male_spaceranger_outs', with elements:
GSM7090416_visium_sham_male_spaceranger_outs_hires_image (Images), GSM7090416_visium_sham_male_spaceranger_outs_lowres_image (Images), GSM7090416_visium_sham_male_spaceranger_outs (Shapes)
▸ 'GSM7090416_visium_sham_male_spaceranger_outs_downscaled_hires', with elements:
GSM7090416_visium_sham_male_spaceranger_outs_hires_image (Images), GSM7090416_visium_sham_male_spaceranger_outs (Shapes)
▸ 'GSM7090416_visium_sham_male_spaceranger_outs_downscaled_lowres', with elements:
GSM7090416_visium_sham_male_spaceranger_outs_lowres_image (Images), GSM7090416_visium_sham_male_spaceranger_outs (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("VVvS0QC3Hcch6qaD") # 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/VVvS0QC3Hcch6qaD
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VVvS0QC3Hcch6qaD Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["VVvS0QC3Hcch6qaD0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- kidney
- Modality
- RNA
- Observations
- 1,815
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,938 px
- mpp
- 3.295 µm/px
- Size
- 19 MB
- Sample ID
- GSM7090416
- License
- unknown
- Published
- Jan 17, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB