Visium
Mouse brain
V52Y23-098
Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_full_image': DataTree[cyx] (3, 2000, 1233), (3, 1000, 616), (3, 500, 308), (3, 250, 154), (3, 125, 77)
│ ├── 'CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_hires_image': DataArray[cyx] (3, 2000, 1233)
│ └── 'CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_lowres_image': DataArray[cyx] (3, 600, 370)
├── Shapes
│ └── 'CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2': GeoDataFrame shape: (5221, 2) (2D shapes)
└── Tables
└── 'table': AnnData (5221, 19465)
with coordinate systems:
▸ 'downscaled_hires', with elements:
CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_hires_image (Images), CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2 (Shapes)
▸ 'downscaled_lowres', with elements:
CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_lowres_image (Images), CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2 (Shapes)
▸ 'global', with elements:
CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2_full_image (Images), CytAssist_FreshFrozen_Mouse_Brain_Post_Xenium_Rep2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("L2mOcUoXkjYM0gJU0002")
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("L2mOcUoXkjYM0gJU") # 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 L2mOcUoXkjYM0gJU0002 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/L2mOcUoXkjYM0gJU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid L2mOcUoXkjYM0gJULicense: CC BY 4.0
Part of collection
Visium CytAssist Gene Expression of Post-Xenium vs Control→ 5 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 5,221
- Chemistry
- Visium CytAssist v2
- Resolution
- 1,233 × 2,000 px
- mpp
- 4.589 µm/px
- Size
- 93.7 MB
- Sample ID
- V52Y23-098
- License
- CC BY 4.0
- Published
- Oct 5, 2023
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB