Visium
Mouse thymus
GSM7679867
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7679867_LJ184_S_003_full_image': DataTree[cyx] (3, 8704, 8448), (3, 4352, 4224), (3, 2176, 2112), (3, 1088, 1056), (3, 544, 528)
│ ├── 'GSM7679867_LJ184_S_003_hires_image': DataArray[cyx] (3, 2000, 1941)
│ └── 'GSM7679867_LJ184_S_003_lowres_image': DataArray[cyx] (3, 600, 583)
├── Shapes
│ └── 'GSM7679867_LJ184_S_003': GeoDataFrame shape: (3010, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3010, 32285)
with coordinate systems:
▸ 'GSM7679867_LJ184_S_003', with elements:
GSM7679867_LJ184_S_003_full_image (Images), GSM7679867_LJ184_S_003_hires_image (Images), GSM7679867_LJ184_S_003_lowres_image (Images), GSM7679867_LJ184_S_003 (Shapes)
▸ 'GSM7679867_LJ184_S_003_downscaled_hires', with elements:
GSM7679867_LJ184_S_003_hires_image (Images), GSM7679867_LJ184_S_003 (Shapes)
▸ 'GSM7679867_LJ184_S_003_downscaled_lowres', with elements:
GSM7679867_LJ184_S_003_lowres_image (Images), GSM7679867_LJ184_S_003 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("LVUIr4QYVnUbpu5Z0000")
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("LVUIr4QYVnUbpu5Z") # 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 LVUIr4QYVnUbpu5Z0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/LVUIr4QYVnUbpu5Z
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LVUIr4QYVnUbpu5ZLicense: NCBI GEO policy
Part of collection
Age-related epithelial defects limit thymic function and regeneration [visium]→ 2 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- thymus
- Modality
- RNA
- Observations (spots)
- 3,010
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 8,448 × 8,704 px
- mpp
- 0.818 µm/px
- Size
- 126 MB
- Sample ID
- GSM7679867
- License
- NCBI GEO policy
- Published
- Jun 27, 2024
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