Visium
Mouse brain
adult-mouse-brain-if-stained-ffpe-1-standard-1-3-0
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_FFPE_Mouse_Brain_IF_full_image': DataTree[cyx] (4, 26624, 25088), (4, 13312, 12544), (4, 6656, 6272), (4, 3328, 3136), (4, 1664, 1568)
│ ├── 'Visium_FFPE_Mouse_Brain_IF_hires_image': DataArray[cyx] (3, 2000, 1885)
│ └── 'Visium_FFPE_Mouse_Brain_IF_lowres_image': DataArray[cyx] (3, 600, 566)
├── Shapes
│ └── 'Visium_FFPE_Mouse_Brain_IF': GeoDataFrame shape: (2438, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2438, 19465)
with coordinate systems:
▸ 'Visium_FFPE_Mouse_Brain_IF', with elements:
Visium_FFPE_Mouse_Brain_IF_full_image (Images), Visium_FFPE_Mouse_Brain_IF_hires_image (Images), Visium_FFPE_Mouse_Brain_IF_lowres_image (Images), Visium_FFPE_Mouse_Brain_IF (Shapes)
▸ 'Visium_FFPE_Mouse_Brain_IF_downscaled_hires', with elements:
Visium_FFPE_Mouse_Brain_IF_hires_image (Images), Visium_FFPE_Mouse_Brain_IF (Shapes)
▸ 'Visium_FFPE_Mouse_Brain_IF_downscaled_lowres', with elements:
Visium_FFPE_Mouse_Brain_IF_lowres_image (Images), Visium_FFPE_Mouse_Brain_IF (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("i7fEEV6whMoAin5W0000")
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("i7fEEV6whMoAin5W") # 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 i7fEEV6whMoAin5W0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/i7fEEV6whMoAin5W
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid i7fEEV6whMoAin5WLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,438
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,885 × 2,000 px
- mpp
- 3.884 µm/px
- Size
- 705 MB
- Sample ID
- adult-mouse-brain-if-stained-ffpe-1-standard-1-3-0
- License
- CC BY 4.0
- Published
- Aug 16, 2021
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