Visium
Mouse kidney
GSM8323123
silver Interactive viewer H&E acute kidney failure No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs': GeoDataFrame shape: (3443, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3443, 19465)
with coordinate systems:
▸ 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs', with elements:
GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_full_image (Images), GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_hires_image (Images), GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_lowres_image (Images), GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs (Shapes)
▸ 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_downscaled_hires', with elements:
GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_hires_image (Images), GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs (Shapes)
▸ 'GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_downscaled_lowres', with elements:
GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs_lowres_image (Images), GSM8323123_visium_day2_male_spaceranger_mouse_day2_outs (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("gh8oCMDt2w5aAksS0000")
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("gh8oCMDt2w5aAksS") # 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 gh8oCMDt2w5aAksS0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/gh8oCMDt2w5aAksS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid gh8oCMDt2w5aAksSLicense: NCBI GEO policy
Part of collection
Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]→ 6 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- kidney
- Condition
- acute kidney failure
- Modality
- RNA
- Observations (spots)
- 3,443
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 3,000 × 3,000 px
- mpp
- 4.284 µm/px
- Size
- 99.9 MB
- Sample ID
- GSM8323123
- License
- NCBI GEO policy
- Published
- Jun 7, 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