Visium
Human oral cavity
Visium spatial transcriptomics data for individual oral squamous cell carcinoma (OSCC) patients (C)
bronze Interactive viewer H&E oral cavity squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'C_hires_image': DataArray[cyx] (3, 1788, 2000)
│ └── 'C_lowres_image': DataArray[cyx] (3, 537, 600)
├── Shapes
│ └── 'C': GeoDataFrame shape: (2872, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2872, 17943)
with coordinate systems:
▸ 'C', with elements:
C_hires_image (Images), C_lowres_image (Images), C (Shapes)
▸ 'C_downscaled_hires', with elements:
C_hires_image (Images), C (Shapes)
▸ 'C_downscaled_lowres', with elements:
C_lowres_image (Images), C (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("fRfHRjx9Q7VW5s1S0000")
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("fRfHRjx9Q7VW5s1S") # 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 fRfHRjx9Q7VW5s1S0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/fRfHRjx9Q7VW5s1S
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid fRfHRjx9Q7VW5s1SLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Vendor
- 10x Genomics
- Organism
- human
- Tissue
- oral cavity
- Condition
- oral cavity squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 2,872
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,788 px
- mpp
- 4.473 µm/px
- Size
- 42.7 MB
- Sample ID
- 29237660:C
- License
- CC BY 4.0
- Published
- Jun 6, 2025
Cite this dataset
doi.org/10.6084/m9.figshare.29237660.v3 ↗ BibTeX
@article{figshare:29237660,
doi = {10.6084/m9.figshare.29237660.v3},
title = {Visium spatial transcriptomics data for individual oral squamous cell carcinoma (OSCC) patients (A)},
year = {2025}
}Source: figshare.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB