Visium HD
Human colon
visium-hd-cytassist-gene-expression-libraries-of-human-crc-v4
silver Interactive viewer H&E colorectal cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_HD_Human_Colon_Cancer_full_image': DataTree[cyx] (3, 48740, 75250), (3, 24370, 37625), (3, 12185, 18812), (3, 6092, 9406), (3, 3046, 4703)
│ ├── 'Visium_HD_Human_Colon_Cancer_hires_image': DataArray[cyx] (3, 3886, 6000)
│ └── 'Visium_HD_Human_Colon_Cancer_lowres_image': DataArray[cyx] (3, 389, 600)
├── Shapes
│ ├── 'Visium_HD_Human_Colon_Cancer_square_002um': GeoDataFrame shape: (8176117, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Colon_Cancer_square_008um': GeoDataFrame shape: (516880, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Colon_Cancer_square_016um': GeoDataFrame shape: (131228, 1) (2D shapes)
│ └── 'Visium_HD_Human_Colon_Cancer_square_016um_for_vitessce': GeoDataFrame shape: (131228, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (8176117, 18132)
├── 'square_008um': AnnData (516880, 18132)
└── 'square_016um': AnnData (131228, 18132)
with coordinate systems:
▸ 'Visium_HD_Human_Colon_Cancer', with elements:
Visium_HD_Human_Colon_Cancer_full_image (Images), Visium_HD_Human_Colon_Cancer_hires_image (Images), Visium_HD_Human_Colon_Cancer_lowres_image (Images), Visium_HD_Human_Colon_Cancer_square_002um (Shapes), Visium_HD_Human_Colon_Cancer_square_008um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Colon_Cancer_downscaled_hires', with elements:
Visium_HD_Human_Colon_Cancer_hires_image (Images), Visium_HD_Human_Colon_Cancer_square_002um (Shapes), Visium_HD_Human_Colon_Cancer_square_008um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Colon_Cancer_downscaled_lowres', with elements:
Visium_HD_Human_Colon_Cancer_lowres_image (Images), Visium_HD_Human_Colon_Cancer_square_002um (Shapes), Visium_HD_Human_Colon_Cancer_square_008um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um (Shapes), Visium_HD_Human_Colon_Cancer_square_016um_for_vitessce (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("EZ7Th4KLErBITmtP") # 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/EZ7Th4KLErBITmtP
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid EZ7Th4KLErBITmtP Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["EZ7Th4KLErBITmtP0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium HD
- Organism
- human
- Tissue
- colon
- Condition
- colorectal cancer
- Modality
- RNA
- Observations
- 516,880
- Tier
- silver
- Chemistry
- Visium HD v1
- Magnification
- 40x
- Resolution
- 75,250 × 48,740 px
- mpp
- 0.274 µm/px
- Size
- 10 GB
- Sample ID
- visium-hd-cytassist-gene-expression-libraries-of-human-crc-v4
- License
- CC BY 4.0
- Published
- Jul 3, 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