Visium
Human colorectum
GSM8703566
bronze Interactive viewer H&E colorectal carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8703566_Tumor26_hires_image': DataArray[cyx] (3, 1817, 2000)
│ └── 'GSM8703566_Tumor26_lowres_image': DataArray[cyx] (3, 545, 600)
├── Shapes
│ └── 'GSM8703566_Tumor26': GeoDataFrame shape: (3415, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3415, 17943)
with coordinate systems:
▸ 'GSM8703566_Tumor26', with elements:
GSM8703566_Tumor26_hires_image (Images), GSM8703566_Tumor26_lowres_image (Images), GSM8703566_Tumor26 (Shapes)
▸ 'GSM8703566_Tumor26_downscaled_hires', with elements:
GSM8703566_Tumor26_hires_image (Images), GSM8703566_Tumor26 (Shapes)
▸ 'GSM8703566_Tumor26_downscaled_lowres', with elements:
GSM8703566_Tumor26_lowres_image (Images), GSM8703566_Tumor26 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("WIs54w6nWccKpx310000")
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("WIs54w6nWccKpx31") # 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 WIs54w6nWccKpx310000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WIs54w6nWccKpx31
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WIs54w6nWccKpx31License: NCBI GEO policy
Part of collection
Fibroblast-Derived Thrombospondin 2 Shapes the Immune-Exclusionary Environment at Invasive Fronts in Colorectal Cancer [Visium→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- colorectum
- Condition
- colorectal carcinoma
- Modality
- RNA
- Observations (spots)
- 3,415
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,817 px
- mpp
- 4.052 µm/px
- Size
- 32.3 MB
- Sample ID
- GSM8703566
- License
- NCBI GEO policy
- Published
- Oct 28, 2025
Cite this dataset
doi.org/10.1038/s41467-025-66485-2 ↗ BibTeX
@article{Iwane_2025,
title = {Targeting fibroblast derived thrombospondin 2 disrupts an immune-exclusionary environment at the tumor front in colorectal cancer},
volume = {16},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-025-66485-2},
DOI = {10.1038/s41467-025-66485-2},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Iwane, Kosuke and Nakanishi, Yuki and Muta, Yu and Chen, Jiayu and Yasumura, Kento and Omatsu, Mayuki and Aoyama, Naoki and Ikeda, Munehiro and Masui, Yoko and Cai, Liyang and Yamakawa, Go and Hamada, Kensuke and Mizukoshi, Kenta and Kawai, Munenori and Iimori, Kei and Nakayama, Shinnosuke and Agatsuma, Nobukazu and Utsumi, Takahiro and Nagao, Munemasa and Maruno, Takahisa and Hiramatsu, Yukiko and Kakiuchi, Nobuyuki and Nakagawa, Masahiro M. and Fukui, Yasuhiro and Kusunoki, Yukina and Kasashima, Hiroaki and Fujimoto, Masakazu and Itatani, Yoshiro and Kogame, Toshiaki and Fukuda, Akihisa and Yashiro, Masakazu and Maeda, Kiyoshi and Kabashima, Kenji and Obama, Kazutaka and Ogawa, Seishi and Diaz-Meco, Maria T. and Moscat, Jorge and Seno, Hiroshi},
year = {2025},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB