Visium
Mouse uterus
GSM8313237
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8313237_S05_hires_image': DataArray[cyx] (3, 2000, 1930)
│ └── 'GSM8313237_S05_lowres_image': DataArray[cyx] (3, 600, 579)
├── Shapes
│ └── 'GSM8313237_S05': GeoDataFrame shape: (207, 2) (2D shapes)
└── Tables
└── 'table': AnnData (207, 50560)
with coordinate systems:
▸ 'GSM8313237_S05', with elements:
GSM8313237_S05_hires_image (Images), GSM8313237_S05_lowres_image (Images), GSM8313237_S05 (Shapes)
▸ 'GSM8313237_S05_downscaled_hires', with elements:
GSM8313237_S05_hires_image (Images), GSM8313237_S05 (Shapes)
▸ 'GSM8313237_S05_downscaled_lowres', with elements:
GSM8313237_S05_lowres_image (Images), GSM8313237_S05 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("x5HVsNnUA3067K1B0000")
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("x5HVsNnUA3067K1B") # 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 x5HVsNnUA3067K1B0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/x5HVsNnUA3067K1B
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid x5HVsNnUA3067K1BLicense: NCBI GEO policy
Part of collection
Cell state dynamics during early stages of serous endometrial carcinoma→ 12 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- uterus
- Modality
- RNA
- Observations (spots)
- 207
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,930 × 2,000 px
- mpp
- 3.413 µm/px
- Size
- 9.6 MB
- Sample ID
- GSM8313237
- License
- NCBI GEO policy
- Published
- Aug 8, 2025
Cite this dataset
doi.org/10.1002/path.6470 ↗ BibTeX
@article{Flesken_Nikitin_2025,
title = {Cell state dynamics during early stages of serous endometrial carcinoma},
volume = {267},
ISSN = {1096-9896},
url = {http://dx.doi.org/10.1002/path.6470},
DOI = {10.1002/path.6470},
number = {3},
journal = {The Journal of Pathology},
publisher = {Wiley},
author = {Flesken‐Nikitin, Andrea and Pirtz, Matalin G and Ashe, Christopher S and Ellenson, Lora H and Yemelyanova, Anna and Cosgrove, Benjamin D and Nikitin, Alexander Yu},
year = {2025},
month = Sept,
pages = {289–303}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB