Visium HD
Mouse kidney
visium-hd-three-prime-mouse-kidney
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_HD_3prime_Mouse_Kidney_full_image': DataTree[cyx] (3, 18663, 28181), (3, 9331, 14090), (3, 4665, 7045), (3, 2332, 3522), (3, 1166, 1761)
│ ├── 'Visium_HD_3prime_Mouse_Kidney_hires_image': DataArray[cyx] (3, 3974, 6000)
│ └── 'Visium_HD_3prime_Mouse_Kidney_lowres_image': DataArray[cyx] (3, 398, 600)
├── Shapes
│ ├── 'Visium_HD_3prime_Mouse_Kidney_square_002um': GeoDataFrame shape: (6753403, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Mouse_Kidney_square_008um': GeoDataFrame shape: (423482, 1) (2D shapes)
│ ├── 'Visium_HD_3prime_Mouse_Kidney_square_016um': GeoDataFrame shape: (106302, 1) (2D shapes)
│ └── 'Visium_HD_3prime_Mouse_Kidney_square_016um_for_vitessce': GeoDataFrame shape: (106302, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (6753403, 33696)
├── 'square_008um': AnnData (423482, 33696)
└── 'square_016um': AnnData (106302, 33696)
with coordinate systems:
▸ 'Visium_HD_3prime_Mouse_Kidney', with elements:
Visium_HD_3prime_Mouse_Kidney_full_image (Images), Visium_HD_3prime_Mouse_Kidney_hires_image (Images), Visium_HD_3prime_Mouse_Kidney_lowres_image (Images), Visium_HD_3prime_Mouse_Kidney_square_002um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_008um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Mouse_Kidney_downscaled_hires', with elements:
Visium_HD_3prime_Mouse_Kidney_hires_image (Images), Visium_HD_3prime_Mouse_Kidney_square_002um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_008um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_3prime_Mouse_Kidney_downscaled_lowres', with elements:
Visium_HD_3prime_Mouse_Kidney_lowres_image (Images), Visium_HD_3prime_Mouse_Kidney_square_002um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_008um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um (Shapes), Visium_HD_3prime_Mouse_Kidney_square_016um_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("S8nURiTjtQ5opsAx0000")
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("S8nURiTjtQ5opsAx") # 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 S8nURiTjtQ5opsAx0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/S8nURiTjtQ5opsAx
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid S8nURiTjtQ5opsAxLicense: CC BY 4.0
Metadata
- Technology
- Visium HD
- Organism
- mouse
- Tissue
- kidney
- Modality
- RNA
- Observations (bins)
- 423,482
- Tier
- silver
- Chemistry
- Visium HD v1
- Magnification
- 40x
- Resolution
- 28,181 × 18,663 px
- mpp
- 0.274 µm/px
- Size
- 2.9 GB
- Sample ID
- visium-hd-three-prime-mouse-kidney
- 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