Visium
Mouse thymus
GSM7823014
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7823014_LJ184_S_016_full_image': DataTree[cyx] (3, 8704, 8192), (3, 4352, 4096), (3, 2176, 2048), (3, 1088, 1024), (3, 544, 512)
│ ├── 'GSM7823014_LJ184_S_016_hires_image': DataArray[cyx] (3, 2000, 1883)
│ └── 'GSM7823014_LJ184_S_016_lowres_image': DataArray[cyx] (3, 600, 565)
├── Shapes
│ └── 'GSM7823014_LJ184_S_016': GeoDataFrame shape: (1612, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1612, 32285)
with coordinate systems:
▸ 'GSM7823014_LJ184_S_016', with elements:
GSM7823014_LJ184_S_016_full_image (Images), GSM7823014_LJ184_S_016_hires_image (Images), GSM7823014_LJ184_S_016_lowres_image (Images), GSM7823014_LJ184_S_016 (Shapes)
▸ 'GSM7823014_LJ184_S_016_downscaled_hires', with elements:
GSM7823014_LJ184_S_016_hires_image (Images), GSM7823014_LJ184_S_016 (Shapes)
▸ 'GSM7823014_LJ184_S_016_downscaled_lowres', with elements:
GSM7823014_LJ184_S_016_lowres_image (Images), GSM7823014_LJ184_S_016 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("4qIX9HVZ5hdvNBIm0000")
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("4qIX9HVZ5hdvNBIm") # 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 4qIX9HVZ5hdvNBIm0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/4qIX9HVZ5hdvNBIm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 4qIX9HVZ5hdvNBImLicense: NCBI GEO policy
Part of collection
Recirculating regulatory T cells mediate thymic regeneration [visium]→ 6 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- thymus
- Modality
- RNA
- Observations (spots)
- 1,612
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 8,192 × 8,704 px
- mpp
- 0.817 µm/px
- Size
- 84.1 MB
- Sample ID
- GSM7823014
- License
- NCBI GEO policy
- Published
- Feb 5, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB