Visium HD
Human lymph node
GSM8658293
bronze Interactive viewer H&E prostate cancer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8658293_SI_38469_hires_image': DataArray[cyx] (3, 5795, 6000)
│ └── 'GSM8658293_SI_38469_lowres_image': DataArray[cyx] (3, 580, 600)
├── Shapes
│ ├── 'GSM8658293_SI_38469_square_008um': GeoDataFrame shape: (162379, 1) (2D shapes)
│ └── 'GSM8658293_SI_38469_square_008um_for_vitessce': GeoDataFrame shape: (162379, 2) (2D shapes)
└── Tables
└── 'square_008um': AnnData (162379, 18085)
with coordinate systems:
▸ 'GSM8658293_SI_38469', with elements:
GSM8658293_SI_38469_hires_image (Images), GSM8658293_SI_38469_lowres_image (Images), GSM8658293_SI_38469_square_008um (Shapes), GSM8658293_SI_38469_square_008um_for_vitessce (Shapes)
▸ 'GSM8658293_SI_38469_downscaled_hires', with elements:
GSM8658293_SI_38469_hires_image (Images), GSM8658293_SI_38469_square_008um (Shapes), GSM8658293_SI_38469_square_008um_for_vitessce (Shapes)
▸ 'GSM8658293_SI_38469_downscaled_lowres', with elements:
GSM8658293_SI_38469_lowres_image (Images), GSM8658293_SI_38469_square_008um (Shapes), GSM8658293_SI_38469_square_008um_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("HiYzMrU5llDCaNSz0002")
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("HiYzMrU5llDCaNSz") # 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 HiYzMrU5llDCaNSz0002 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/HiYzMrU5llDCaNSz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid HiYzMrU5llDCaNSzLicense: NCBI GEO policy
Part of collection
CDK12/13 inactivation triggers STING-mediated antitumor immunity in preclinical models→ 4 datasets · comparison
Metadata
- Technology
- Visium HD
- Organism
- human
- Tissue
- lymph node
- Condition
- prostate cancer
- Modality
- RNA
- Observations (bins)
- 162,379
- Tier
- bronze
- Resolution
- 6,000 × 5,795 px
- mpp
- 1.603 µm/px
- Size
- 260 MB
- Sample ID
- GSM8658293
- License
- NCBI GEO policy
- Published
- Jun 23, 2025
Cite this dataset
doi.org/10.1172/jci193745 ↗ BibTeX
@article{Bao_2025,
title = {CDK12/13 inactivation triggers STING-mediated antitumor immunity in preclinical models},
volume = {135},
ISSN = {1558-8238},
url = {http://dx.doi.org/10.1172/jci193745},
DOI = {10.1172/jci193745},
number = {18},
journal = {Journal of Clinical Investigation},
publisher = {American Society for Clinical Investigation},
author = {Bao, Yi and Chang, Yu and Tien, Jean Ching-Yi and Cruz, Gabriel and Yang, Fan and Mannan, Rahul and Mahapatra, Somnath and Paturu, Radha and Cao, Xuhong and Su, Fengyun and Wang, Rui and Zhang, Yuping and Gondal, Mahnoor and Choi, Jae Eun and Gurkan, Jonathan K. and Miner, Stephanie J. and Robinson, Dan R. and Wu, Yi-Mi and Zhou, Licheng and Wang, Zhen and Kryczek, Ilona and Wang, Xiaoju and Cieslik, Marcin and Qiao, Yuanyuan and Tsodikov, Alexander and Zou, Weiping and Ding, Ke and Chinnaiyan, Arul M.},
year = {2025},
month = July
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB