Visium
Human breast
GSM8662120
bronze Interactive viewer H&E metaplastic breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8662120_VLP68D_hires_image': DataArray[cyx] (3, 2000, 1932)
│ └── 'GSM8662120_VLP68D_lowres_image': DataArray[cyx] (3, 600, 580)
├── Shapes
│ └── 'GSM8662120_VLP68D': GeoDataFrame shape: (4240, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4240, 17943)
with coordinate systems:
▸ 'GSM8662120_VLP68D', with elements:
GSM8662120_VLP68D_hires_image (Images), GSM8662120_VLP68D_lowres_image (Images), GSM8662120_VLP68D (Shapes)
▸ 'GSM8662120_VLP68D_downscaled_hires', with elements:
GSM8662120_VLP68D_hires_image (Images), GSM8662120_VLP68D (Shapes)
▸ 'GSM8662120_VLP68D_downscaled_lowres', with elements:
GSM8662120_VLP68D_lowres_image (Images), GSM8662120_VLP68D (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("z6E2xjKE5zhzzwFB0000")
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("z6E2xjKE5zhzzwFB") # 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 z6E2xjKE5zhzzwFB0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/z6E2xjKE5zhzzwFB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid z6E2xjKE5zhzzwFBLicense: NCBI GEO policy
Part of collection
Integrated Methylation and Spatial Transcriptomic Profiling of Metaplastic Breast Cancer to Investigate Intra-tumoral Heterogeneity.→ 8 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- metaplastic breast carcinoma
- Modality
- RNA
- Observations (spots)
- 4,240
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,932 × 2,000 px
- mpp
- 3.248 µm/px
- Size
- 18.5 MB
- Sample ID
- GSM8662120
- License
- NCBI GEO policy
- Published
- Aug 12, 2025
Cite this dataset
doi.org/10.1038/s41523-025-00807-x ↗ BibTeX
@article{Feng_2025,
title = {Integrated profiling of metaplastic breast cancer identifies putative master regulators of intratumoral heterogeneity},
volume = {11},
ISSN = {2374-4677},
url = {http://dx.doi.org/10.1038/s41523-025-00807-x},
DOI = {10.1038/s41523-025-00807-x},
number = {1},
journal = {npj Breast Cancer},
publisher = {Springer Science and Business Media LLC},
author = {Feng, Yufan and Xiong, Albert and Mulay, Onkar and Sokolova, Anna and Lim, Malcolm and Van Haeringen, Benjamin and McGuire, Natasha and de Luca, Xavier and Simpson, Peter T. and Nguyen, Quan and Lakhani, Sunil R. and McCart Reed, Amy E.},
year = {2025},
month = Aug
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB