Visium
Human colon
GSM9322960
silver Interactive viewer H&E colorectal carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9322960_TR11_21723_hires_image': DataArray[cyx] (3, 1299, 2000)
│ └── 'GSM9322960_TR11_21723_lowres_image': DataArray[cyx] (3, 390, 600)
├── Shapes
│ └── 'GSM9322960_TR11_21723': GeoDataFrame shape: (4362, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4362, 18085)
with coordinate systems:
▸ 'GSM9322960_TR11_21723', with elements:
GSM9322960_TR11_21723_hires_image (Images), GSM9322960_TR11_21723_lowres_image (Images), GSM9322960_TR11_21723 (Shapes)
▸ 'GSM9322960_TR11_21723_downscaled_hires', with elements:
GSM9322960_TR11_21723_hires_image (Images), GSM9322960_TR11_21723 (Shapes)
▸ 'GSM9322960_TR11_21723_downscaled_lowres', with elements:
GSM9322960_TR11_21723_lowres_image (Images), GSM9322960_TR11_21723 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("rDBWjvddZYTELxem0000")
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("rDBWjvddZYTELxem") # 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 rDBWjvddZYTELxem0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/rDBWjvddZYTELxem
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rDBWjvddZYTELxemLicense: NCBI GEO policy
Part of collection
Collagen Alignment and Spatial Transcriptomics Analysis (CASTA) reveals gene programs associated with collagen alignmet in colorectal cancer→ 5 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- colon
- Condition
- colorectal carcinoma
- Modality
- RNA
- Observations (spots)
- 4,362
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,299 px
- mpp
- 10.051 µm/px
- Size
- 31.5 MB
- Sample ID
- GSM9322960
- License
- NCBI GEO policy
- Published
- Nov 29, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB