Visium

Human brain

GSM7507316

bronze Interactive viewer H&E glioblastoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM7507316_ST_Pt5_Pt7_hires_image': DataArray[cyx] (3, 2000, 1820)
│     └── 'GSM7507316_ST_Pt5_Pt7_lowres_image': DataArray[cyx] (3, 600, 546)
├── Shapes
│     └── 'GSM7507316_ST_Pt5_Pt7': GeoDataFrame shape: (2560, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2560, 33538)
with coordinate systems:
    ▸ 'GSM7507316_ST_Pt5_Pt7', with elements:
        GSM7507316_ST_Pt5_Pt7_hires_image (Images), GSM7507316_ST_Pt5_Pt7_lowres_image (Images), GSM7507316_ST_Pt5_Pt7 (Shapes)
    ▸ 'GSM7507316_ST_Pt5_Pt7_downscaled_hires', with elements:
        GSM7507316_ST_Pt5_Pt7_hires_image (Images), GSM7507316_ST_Pt5_Pt7 (Shapes)
    ▸ 'GSM7507316_ST_Pt5_Pt7_downscaled_lowres', with elements:
        GSM7507316_ST_Pt5_Pt7_lowres_image (Images), GSM7507316_ST_Pt5_Pt7 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("ZE2oJEg41PiIcw4y0000")
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("ZE2oJEg41PiIcw4y")   # 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 ZE2oJEg41PiIcw4y0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZE2oJEg41PiIcw4y

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZE2oJEg41PiIcw4y

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Siglec-9 acts as an immune checkpoint molecule on macrophages in glioblastoma, restricting T cell priming and immunotherapy response [ST]→

20 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: brain
Condition: glioblastoma
Modality: RNA
Observations (spots): 2,560
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 1,820 × 2,000 px
mpp: 3.759 µm/px
Size: 40.9 MB
Sample ID: GSM7507316
License: NCBI GEO policy
Published: Jun 29, 2023

Cite this dataset

doi.org/10.1038/s43018-023-00598-9 ↗

BibTeX

@article{Mei_2023,
  title = {Siglec-9 acts as an immune-checkpoint molecule on macrophages in glioblastoma, restricting T-cell priming and immunotherapy response},
  volume = {4},
  ISSN = {2662-1347},
  url = {http://dx.doi.org/10.1038/s43018-023-00598-9},
  DOI = {10.1038/s43018-023-00598-9},
  number = {9},
  journal = {Nature Cancer},
  publisher = {Springer Science and Business Media LLC},
  author = {Mei, Yan and Wang, Xiumei and Zhang, Ji and Liu, Dan and He, Junjie and Huang, Chunliu and Liao, Jing and Wang, Yingzhao and Feng, Yongyi and Li, Hongyu and Liu, Xiuying and Chen, Lingdan and Yi, Wei and Chen, Xi and Bai, Hong-Min and Wang, Xinyu and Li, Yiyi and Wang, Lixiang and Liang, Zhigang and Ren, Xianwen and Qiu, Li and Hui, Yuan and Zhang, Qingling and Leng, Qibin and Chen, Jun and Jia, Guangshuai},
  year = {2023},
  month = July,
  pages = {1273–1291}
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB