Visium
Human midbrain
GSM8608415
bronze Interactive viewer H&E diffuse intrinsic pontine glioma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8608415_VLP73_D1_hires_image': DataArray[cyx] (3, 2000, 1276)
│ └── 'GSM8608415_VLP73_D1_lowres_image': DataArray[cyx] (3, 600, 383)
├── Shapes
│ └── 'GSM8608415_VLP73_D1': GeoDataFrame shape: (3658, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3658, 18085)
with coordinate systems:
▸ 'GSM8608415_VLP73_D1', with elements:
GSM8608415_VLP73_D1_hires_image (Images), GSM8608415_VLP73_D1_lowres_image (Images), GSM8608415_VLP73_D1 (Shapes)
▸ 'GSM8608415_VLP73_D1_downscaled_hires', with elements:
GSM8608415_VLP73_D1_hires_image (Images), GSM8608415_VLP73_D1 (Shapes)
▸ 'GSM8608415_VLP73_D1_downscaled_lowres', with elements:
GSM8608415_VLP73_D1_lowres_image (Images), GSM8608415_VLP73_D1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("wq978RZe52qwucjo0000")
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("wq978RZe52qwucjo") # 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 wq978RZe52qwucjo0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/wq978RZe52qwucjo
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid wq978RZe52qwucjoLicense: NCBI GEO policy
Part of collection
Spatial Analysis of a Complete DIPG-Infiltrated Brainstem Reveals Novel Ligand-Receptor Mediators of Tumor-to-TME Crosstalk→ 10 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- midbrain
- Condition
- diffuse intrinsic pontine glioma
- Modality
- RNA
- Observations (spots)
- 3,658
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,276 × 2,000 px
- mpp
- 4.807 µm/px
- Size
- 62.8 MB
- Sample ID
- GSM8608415
- License
- NCBI GEO policy
- Published
- Nov 18, 2024
Cite this dataset
doi.org/10.1186/s40478-025-01952-x ↗ BibTeX
@article{Kordowski_2025,
title = {Spatial analysis of a complete DIPG-infiltrated brainstem reveals novel ligand-receptor mediators of tumour-to-TME crosstalk},
volume = {13},
ISSN = {2051-5960},
url = {http://dx.doi.org/10.1186/s40478-025-01952-x},
DOI = {10.1186/s40478-025-01952-x},
number = {1},
journal = {Acta Neuropathologica Communications},
publisher = {Springer Science and Business Media LLC},
author = {Kordowski, Anja and Mulay, Onkar and Tan, Xiao and Vo, Tuan and Baumgartner, Ulrich and Maybury, Mellissa K. and Hassall, Timothy and Harris, Lachlan and Nguyen, Quan and Day, Bryan W.},
year = {2025},
month = Feb
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB