Visium
Human colon
visium-cytassist-human-colon-normal-p3
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_V2_Human_Colon_Normal_P3_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'Visium_V2_Human_Colon_Normal_P3_hires_image': DataArray[cyx] (3, 2019, 4000)
│ └── 'Visium_V2_Human_Colon_Normal_P3_lowres_image': DataArray[cyx] (3, 303, 600)
├── Shapes
│ └── 'Visium_V2_Human_Colon_Normal_P3': GeoDataFrame shape: (3887, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3887, 18085)
with coordinate systems:
▸ 'Visium_V2_Human_Colon_Normal_P3', with elements:
Visium_V2_Human_Colon_Normal_P3_full_image (Images), Visium_V2_Human_Colon_Normal_P3_hires_image (Images), Visium_V2_Human_Colon_Normal_P3_lowres_image (Images), Visium_V2_Human_Colon_Normal_P3 (Shapes)
▸ 'Visium_V2_Human_Colon_Normal_P3_downscaled_hires', with elements:
Visium_V2_Human_Colon_Normal_P3_hires_image (Images), Visium_V2_Human_Colon_Normal_P3 (Shapes)
▸ 'Visium_V2_Human_Colon_Normal_P3_downscaled_lowres', with elements:
Visium_V2_Human_Colon_Normal_P3_lowres_image (Images), Visium_V2_Human_Colon_Normal_P3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ETm3REX6qjG180pe0000")
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("ETm3REX6qjG180pe") # 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 ETm3REX6qjG180pe0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ETm3REX6qjG180pe
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ETm3REX6qjG180peLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- colon
- Modality
- RNA
- Observations (spots)
- 3,887
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 4,000 × 2,019 px
- mpp
- 5.880 µm/px
- Size
- 67.7 MB
- Sample ID
- visium-cytassist-human-colon-normal-p3
- License
- CC BY 4.0
- Published
- May 15, 2023
Cite this dataset
doi.org/10.1038/s41588-025-02193-3 ↗ BibTeX
@article{Oliveira_2025,
title = {High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer},
volume = {57},
ISSN = {1546-1718},
url = {http://dx.doi.org/10.1038/s41588-025-02193-3},
DOI = {10.1038/s41588-025-02193-3},
number = {6},
journal = {Nature Genetics},
publisher = {Springer Science and Business Media LLC},
author = {Oliveira, Michelli Faria de and Romero, Juan Pablo and Chung, Meii and Williams, Stephen R. and Gottscho, Andrew D. and Gupta, Anushka and Pilipauskas, Susan E. and Mohabbat, Seayar and Raman, Nandhini and Sukovich, David J. and Patterson, David M. and de Oliveira, Michelli Faria and Romero, Juan Pablo and Williams, Stephen R. and Patterson, David M. and Taylor, Sarah E. B. and Taylor, Sarah E. B.},
year = {2025},
month = June,
pages = {1512–1523}
}Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB