Visium
Human brain
GSM8428202
bronze Interactive viewer H&E glioblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8428202_GBM3_hires_image': DataArray[cyx] (3, 1591, 2000)
│ └── 'GSM8428202_GBM3_lowres_image': DataArray[cyx] (3, 477, 600)
├── Shapes
│ └── 'GSM8428202_GBM3': GeoDataFrame shape: (4635, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4635, 18085)
with coordinate systems:
▸ 'GSM8428202_GBM3', with elements:
GSM8428202_GBM3_hires_image (Images), GSM8428202_GBM3_lowres_image (Images), GSM8428202_GBM3 (Shapes)
▸ 'GSM8428202_GBM3_downscaled_hires', with elements:
GSM8428202_GBM3_hires_image (Images), GSM8428202_GBM3 (Shapes)
▸ 'GSM8428202_GBM3_downscaled_lowres', with elements:
GSM8428202_GBM3_lowres_image (Images), GSM8428202_GBM3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ZdcE1yTLRUXusWXl0000")
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("ZdcE1yTLRUXusWXl") # 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 ZdcE1yTLRUXusWXl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZdcE1yTLRUXusWXl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZdcE1yTLRUXusWXlLicense: NCBI GEO policy
Part of collection
The roles of glioma-associated macrophages/microglia in human GBM→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- glioblastoma
- Modality
- RNA
- Observations (spots)
- 4,635
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,591 px
- mpp
- 4.701 µm/px
- Size
- 82.4 MB
- Sample ID
- GSM8428202
- License
- NCBI GEO policy
- Published
- Apr 11, 2025
Cite this dataset
doi.org/10.1111/cas.70014 ↗ BibTeX
@article{Matsuzaki_2025,
title = {Abnormal Vessels Potentially Accelerate Glioblastoma Proliferation by Inducing the Protumor Activation of Macrophages},
volume = {116},
ISSN = {1349-7006},
url = {http://dx.doi.org/10.1111/cas.70014},
DOI = {10.1111/cas.70014},
number = {4},
journal = {Cancer Science},
publisher = {Wiley},
author = {Matsuzaki, Hiroaki and Kai, Keitaro and Komohara, Yoshihiro and Yano, Hiromu and Pan, Cheng and Fujiwara, Yukio and Yamada, Rin and Iwauchi, Ai and Fukasawa, Nei and Tanaka, Toshihide and Shimoda, Masayuki and Watanabe, Hiroshi and Maruyama, Toru and Takeo, Toru and Mikami, Yoshiki and Mukasa, Akitake},
year = {2025},
month = Feb,
pages = {897–909}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB