Visium

Human liver

GSM8155175

bronze Interactive viewer H&E hepatoblastoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8155175_H388_hires_image': DataArray[cyx] (3, 1905, 2000)
│     └── 'GSM8155175_H388_lowres_image': DataArray[cyx] (3, 572, 600)
├── Shapes
│     └── 'GSM8155175_H388': GeoDataFrame shape: (3333, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3333, 17943)
with coordinate systems:
    ▸ 'GSM8155175_H388', with elements:
        GSM8155175_H388_hires_image (Images), GSM8155175_H388_lowres_image (Images), GSM8155175_H388 (Shapes)
    ▸ 'GSM8155175_H388_downscaled_hires', with elements:
        GSM8155175_H388_hires_image (Images), GSM8155175_H388 (Shapes)
    ▸ 'GSM8155175_H388_downscaled_lowres', with elements:
        GSM8155175_H388_lowres_image (Images), GSM8155175_H388 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("4aeTpJBEtlkq5fnz0000")
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("4aeTpJBEtlkq5fnz")   # 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 4aeTpJBEtlkq5fnz0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/4aeTpJBEtlkq5fnz

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 4aeTpJBEtlkq5fnz

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [Spatial Transcriptomics]→

22 datasets · other

Metadata

Technology: Visium
Organism: human
Tissue: liver
Condition: hepatoblastoma
Modality: RNA
Observations (spots): 3,333
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,905 px
mpp: 3.509 µm/px
Size: 52.1 MB
Sample ID: GSM8155175
License: NCBI GEO policy
Published: Feb 7, 2025

Cite this dataset

doi.org/10.1016/j.jhep.2025.01.031 ↗

BibTeX

@article{M_nter_2025,
  title = {Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma},
  volume = {83},
  ISSN = {0168-8278},
  url = {http://dx.doi.org/10.1016/j.jhep.2025.01.031},
  DOI = {10.1016/j.jhep.2025.01.031},
  number = {2},
  journal = {Journal of Hepatology},
  publisher = {Elsevier BV},
  author = {Münter, Daniel and de Faria, Flavia W. and Richter, Mathis and Aranda-Pardos, Irene and Hotfilder, Marc and Walter, Carolin and Paga, Enya and Inserte, Clara and Albert, Thomas K. and Roy, Rajanya and Rahman, Shariyah and Riedel, Nicole C. and Müller, Volker and Pascher, Andreas and Wiebe, Karsten and Schmid, Irene and Vokuhl, Christian and Winkler, Beate and Jüttner, Eva and Vieth, Simon and Mücke, Urs and Kluiver, Thomas A. and Peng, Weng Chuan and Rossig, Claudia and Schlué, Jerome and Madadi-Sanjani, Omid and Sandmann, Sarah and Hartmann, Wolfgang and A-Gonzalez, Noelia and Soehnlein, Oliver and Kerl, Kornelius},
  year = {2025},
  month = Aug,
  pages = {367–382}
}

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