Visium

Human brain

GSM8428199

bronze Interactive viewer H&E glioblastoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8428199_A_hires_image': DataArray[cyx] (3, 1930, 2000)
│     └── 'GSM8428199_A_lowres_image': DataArray[cyx] (3, 579, 600)
├── Shapes
│     └── 'GSM8428199_A': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 18085)
with coordinate systems:
    ▸ 'GSM8428199_A', with elements:
        GSM8428199_A_hires_image (Images), GSM8428199_A_lowres_image (Images), GSM8428199_A (Shapes)
    ▸ 'GSM8428199_A_downscaled_hires', with elements:
        GSM8428199_A_hires_image (Images), GSM8428199_A (Shapes)
    ▸ 'GSM8428199_A_downscaled_lowres', with elements:
        GSM8428199_A_lowres_image (Images), GSM8428199_A (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("se8NSSMygUpdsSPs0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("se8NSSMygUpdsSPs")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download se8NSSMygUpdsSPs0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/se8NSSMygUpdsSPs

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid se8NSSMygUpdsSPs

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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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): 4,992
Tier: bronze
Chemistry: Visium v1
Resolution: 2,000 × 1,930 px
mpp: 4.198 µm/px
Size: 109 MB
Sample ID: GSM8428199
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