Visium HD
Mouse jejunum
GSM9134409
silver Interactive viewer H&E radiation-induced disorder No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM9134409_rep3_hires_image': DataArray[cyx] (3, 5110, 6000)
│ └── 'GSM9134409_rep3_lowres_image': DataArray[cyx] (3, 511, 600)
├── Shapes
│ ├── 'GSM9134409_rep3_square_008um': GeoDataFrame shape: (398382, 1) (2D shapes)
│ └── 'GSM9134409_rep3_square_008um_for_vitessce': GeoDataFrame shape: (398382, 2) (2D shapes)
└── Tables
└── 'square_008um': AnnData (398382, 19059)
with coordinate systems:
▸ 'GSM9134409_rep3', with elements:
GSM9134409_rep3_hires_image (Images), GSM9134409_rep3_lowres_image (Images), GSM9134409_rep3_square_008um (Shapes), GSM9134409_rep3_square_008um_for_vitessce (Shapes)
▸ 'GSM9134409_rep3_downscaled_hires', with elements:
GSM9134409_rep3_hires_image (Images), GSM9134409_rep3_square_008um (Shapes), GSM9134409_rep3_square_008um_for_vitessce (Shapes)
▸ 'GSM9134409_rep3_downscaled_lowres', with elements:
GSM9134409_rep3_lowres_image (Images), GSM9134409_rep3_square_008um (Shapes), GSM9134409_rep3_square_008um_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("kZrFcCzX518qDCgu0000")
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("kZrFcCzX518qDCgu") # 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 kZrFcCzX518qDCgu0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kZrFcCzX518qDCgu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kZrFcCzX518qDCguLicense: NCBI GEO policy
Part of collection
A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration in the Jejunum→ 4 datasets · comparison
Metadata
- Technology
- Visium HD
- Organism
- mouse
- Tissue
- jejunum
- Condition
- radiation-induced disorder
- Modality
- RNA
- Observations (bins)
- 398,382
- Tier
- silver
- Resolution
- 6,000 × 5,110 px
- mpp
- 2.682 µm/px
- Size
- 1.0 GB
- Sample ID
- GSM9134409
- License
- NCBI GEO policy
- Published
- Jul 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