Visium HD
Arabidopsis thaliana multicellular organism
visium-hd-three-prime-arabidopsis
H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_HD_3prime_Arabidopsis_full_image': DataTree[cyx] (3, 18329, 16138), (3, 9164, 8069), (3, 4582, 4034), (3, 2291, 2017), (3, 1145, 1008)
│ ├── 'Visium_HD_3prime_Arabidopsis_hires_image': DataArray[cyx] (3, 6000, 5283)
│ └── 'Visium_HD_3prime_Arabidopsis_lowres_image': DataArray[cyx] (3, 600, 528)
├── Shapes
│ ├── 'Visium_HD_3prime_Arabidopsis_square_002um': GeoDataFrame shape: (117696, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Arabidopsis_square_008um': GeoDataFrame shape: (7356, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Arabidopsis_square_016um': GeoDataFrame shape: (2089, 1) (2D shapes)
│ └── 'Visium_HD_3prime_Arabidopsis_square_016um_for_vitessce': GeoDataFrame shape: (2089, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (117696, 31109)
├── 'square_008um': AnnData (7356, 31109)
└── 'square_016um': AnnData (2089, 31109)
with coordinate systems:
▸ 'Visium_HD_3prime_Arabidopsis', with elements:
Visium_HD_3prime_Arabidopsis_full_image (Images), Visium_HD_3prime_Arabidopsis_hires_image (Images), Visium_HD_3prime_Arabidopsis_lowres_image (Images), Visium_HD_3prime_Arabidopsis_square_002um (Shapes), Visium_HD_3prime_Arabidopsis_square_008um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Arabidopsis_downscaled_hires', with elements:
Visium_HD_3prime_Arabidopsis_hires_image (Images), Visium_HD_3prime_Arabidopsis_square_002um (Shapes), Visium_HD_3prime_Arabidopsis_square_008um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Arabidopsis_downscaled_lowres', with elements:
Visium_HD_3prime_Arabidopsis_lowres_image (Images), Visium_HD_3prime_Arabidopsis_square_002um (Shapes), Visium_HD_3prime_Arabidopsis_square_008um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um (Shapes), Visium_HD_3prime_Arabidopsis_square_016um_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("xMVNylUKjgYbVzDw0000")
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("xMVNylUKjgYbVzDw") # 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 xMVNylUKjgYbVzDw0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/xMVNylUKjgYbVzDw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xMVNylUKjgYbVzDwLicense: CC BY 4.0
Metadata
- Technology
- Visium HD
- Organism
- arabidopsis thaliana
- Tissue
- multicellular organism
- Modality
- RNA
- Chemistry
- Visium HD v1
- Staining
- H&E
- Magnification
- 40x
- Resolution
- 16,138 × 18,329 px
- mpp
- 0.274 µm/px
- Size
- 536 MB
- Sample ID
- visium-hd-three-prime-arabidopsis
- License
- CC BY 4.0
- Published
- Oct 13, 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