Visium HD
Mouse embryo
visium-hd-three-prime-mouse-embryo-fresh-frozen
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_HD_3prime_Mouse_Embryo_full_image': DataTree[cyx] (3, 38147, 48978), (3, 19073, 24489), (3, 9536, 12244), (3, 4768, 6122), (3, 2384, 3061)
│ ├── 'Visium_HD_3prime_Mouse_Embryo_hires_image': DataArray[cyx] (3, 4673, 6000)
│ └── 'Visium_HD_3prime_Mouse_Embryo_lowres_image': DataArray[cyx] (3, 468, 600)
├── Shapes
│ ├── 'Visium_HD_3prime_Mouse_Embryo_square_002um': GeoDataFrame shape: (8685416, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Mouse_Embryo_square_008um': GeoDataFrame shape: (543180, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Mouse_Embryo_square_016um': GeoDataFrame shape: (136130, 1) (2D shapes)
│ └── 'Visium_HD_3prime_Mouse_Embryo_square_016um_for_vitessce': GeoDataFrame shape: (136130, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (8685416, 33696)
├── 'square_008um': AnnData (543180, 33696)
└── 'square_016um': AnnData (136130, 33696)
with coordinate systems:
▸ 'Visium_HD_3prime_Mouse_Embryo', with elements:
Visium_HD_3prime_Mouse_Embryo_full_image (Images), Visium_HD_3prime_Mouse_Embryo_hires_image (Images), Visium_HD_3prime_Mouse_Embryo_lowres_image (Images), Visium_HD_3prime_Mouse_Embryo_square_002um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_008um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Mouse_Embryo_downscaled_hires', with elements:
Visium_HD_3prime_Mouse_Embryo_hires_image (Images), Visium_HD_3prime_Mouse_Embryo_square_002um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_008um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Mouse_Embryo_downscaled_lowres', with elements:
Visium_HD_3prime_Mouse_Embryo_lowres_image (Images), Visium_HD_3prime_Mouse_Embryo_square_002um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_008um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um (Shapes), Visium_HD_3prime_Mouse_Embryo_square_016um_for_vitessce (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Mw0hNHKwJhGcnqcA") # 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/Mw0hNHKwJhGcnqcA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Mw0hNHKwJhGcnqcA Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Mw0hNHKwJhGcnqcA0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium HD
- Organism
- mouse
- Tissue
- embryo
- Modality
- RNA
- Observations
- 543,180
- Tier
- silver
- Chemistry
- Visium HD v1
- Magnification
- 40x
- Resolution
- 48,978 × 38,147 px
- mpp
- 0.274 µm/px
- Size
- 6.1 GB
- Sample ID
- visium-hd-three-prime-mouse-embryo-fresh-frozen
- License
- CC BY 4.0
- Published
- Jun 10, 2025
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