Visium
Human skin of body
GSM8797977
bronze Interactive viewer H&E skin squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8797977_S3_SpT_hires_image': DataArray[cyx] (3, 2000, 1949)
│ └── 'GSM8797977_S3_SpT_lowres_image': DataArray[cyx] (3, 600, 585)
├── Shapes
│ └── 'GSM8797977_S3_SpT': GeoDataFrame shape: (2887, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2887, 17943)
with coordinate systems:
▸ 'GSM8797977_S3_SpT', with elements:
GSM8797977_S3_SpT_hires_image (Images), GSM8797977_S3_SpT_lowres_image (Images), GSM8797977_S3_SpT (Shapes)
▸ 'GSM8797977_S3_SpT_downscaled_hires', with elements:
GSM8797977_S3_SpT_hires_image (Images), GSM8797977_S3_SpT (Shapes)
▸ 'GSM8797977_S3_SpT_downscaled_lowres', with elements:
GSM8797977_S3_SpT_lowres_image (Images), GSM8797977_S3_SpT (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("w2pA2JrsjtgNwXWC0000")
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("w2pA2JrsjtgNwXWC") # 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 w2pA2JrsjtgNwXWC0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/w2pA2JrsjtgNwXWC
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid w2pA2JrsjtgNwXWCLicense: NCBI GEO policy
Part of collection
Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [Spatial Transcriptomics]→ 11 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- skin squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 2,887
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,949 × 2,000 px
- mpp
- 3.525 µm/px
- Size
- 56.2 MB
- Sample ID
- GSM8797977
- License
- NCBI GEO policy
- Published
- Aug 20, 2025
Cite this dataset
doi.org/10.1038/s41586-025-09370-8 ↗ BibTeX
@article{Baruch_2025,
title = {Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy},
volume = {646},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-025-09370-8},
DOI = {10.1038/s41586-025-09370-8},
number = {8084},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Baruch, Erez N. and Gleber-Netto, Frederico O. and Nagarajan, Priyadharsini and Rao, Xiayu and Akhter, Shamima and Eichwald, Tuany and Xie, Tongxin and Balood, Mohammad and Adewale, Adebayo and Naara, Shorook and Sathishkumar, Hinduja N. and Islam, Shajedul and McCarthy, William and Mattson, Brandi J. and Ferrarotto, Renata and Wong, Michael K. and Davies, Michael A. and Jindal, Sonali and Basu, Sreyashi and Roversi, Karine and Nikpoor, Amin Reza and Ahmadi, Maryam and Ahmadi, Ali and Harwood, Catherine and Leigh, Irene and Gong, Dennis and Tallón de Lara, Paulino and Tao, Derrick L. and Davidson, Tara M. and Ajami, Nadim J. and Futreal, Andrew and Rai, Kunal and Kochat, Veena and Castillo, Micah and Gunaratne, Preethi and Goepfert, Ryan P. and Hernandez, Sharia D. and Khushalani, Nikhil I. and Wang, Jing and Watowich, Stephanie S. and Calin, George A. and Migden, Michael R. and Yuan, Mona and Liu, Naijiang and Ye, Yi and Hwang, William L. and Vermeer, Paola D. and D’Silva, Nisha J. and Bunimovich, Yuri L. and Yaniv, Dan and Burks, Jared K. and Gomez, Javier and Dougherty, Patrick M. and Tsai, Kenneth Y. and Allison, James P. and Sharma, Padmanee and Wargo, Jennifer A. and Myers, Jeffrey N. and Talbot, Sebastien and Gross, Neil D. and Amit, Moran},
year = {2025},
month = Aug,
pages = {462–473}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB