Visium
Human kidney
GSE261545
bronze Interactive viewer H&E diabetic kidney disease Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8146484_DKD1_hires_image': DataArray[cyx] (3, 2000, 1781)
│ └── 'GSM8146484_DKD1_lowres_image': DataArray[cyx] (3, 600, 534)
├── Shapes
│ └── 'GSM8146484_DKD1': GeoDataFrame shape: (2802, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2802, 18085)
with coordinate systems:
▸ 'GSM8146484_DKD1', with elements:
GSM8146484_DKD1_hires_image (Images), GSM8146484_DKD1_lowres_image (Images), GSM8146484_DKD1 (Shapes)
▸ 'GSM8146484_DKD1_downscaled_hires', with elements:
GSM8146484_DKD1_hires_image (Images), GSM8146484_DKD1 (Shapes)
▸ 'GSM8146484_DKD1_downscaled_lowres', with elements:
GSM8146484_DKD1_lowres_image (Images), GSM8146484_DKD1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("2Px4hjJFRq22eikg0000")
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("2Px4hjJFRq22eikg") # 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 2Px4hjJFRq22eikg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/2Px4hjJFRq22eikg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 2Px4hjJFRq22eikgLicense: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Condition
- diabetic kidney disease
- Modality
- RNA
- Observations (spots)
- 2,802
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,781 × 2,000 px
- mpp
- 3.785 µm/px
- Size
- 62.8 MB
- Sample ID
- GSE261545
- License
- NCBI GEO policy
- Published
- Jun 27, 2024
Cite this dataset
doi.org/10.1016/j.ajpath.2024.06.011 ↗ BibTeX
@article{geo:GSE261545,
doi = {10.1016/j.ajpath.2024.06.011},
title = {GSE261545},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB