Visium HD

Human liver

GSM9521683

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9521683_Arc-Liver-D1_002um_cytassist_image': DataArray[cyx] (3, 2999, 3201)
│     ├── 'GSM9521683_Arc-Liver-D1_002um_hires_image': DataArray[cyx] (3, 6000, 5302)
│     └── 'GSM9521683_Arc-Liver-D1_002um_lowres_image': DataArray[cyx] (3, 600, 530)
├── Shapes
│     ├── 'GSM9521683_Arc-Liver-D1_002um_square_002um': GeoDataFrame shape: (5244110, 1) (2D shapes)
│     ├── 'GSM9521683_Arc-Liver-D1_002um_square_008um': GeoDataFrame shape: (333667, 1) (2D shapes)
│     ├── 'GSM9521683_Arc-Liver-D1_002um_square_016um': GeoDataFrame shape: (85292, 1) (2D shapes)
│     └── 'GSM9521683_Arc-Liver-D1_002um_square_016um_for_vitessce': GeoDataFrame shape: (85292, 2) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (5244110, 18132)
      ├── 'square_008um': AnnData (333667, 18132)
      └── 'square_016um': AnnData (85292, 18132)
with coordinate systems:
    ▸ 'GSM9521683_Arc-Liver-D1_002um', with elements:
        GSM9521683_Arc-Liver-D1_002um_cytassist_image (Images), GSM9521683_Arc-Liver-D1_002um_hires_image (Images), GSM9521683_Arc-Liver-D1_002um_lowres_image (Images), GSM9521683_Arc-Liver-D1_002um_square_002um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_008um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM9521683_Arc-Liver-D1_002um_downscaled_hires', with elements:
        GSM9521683_Arc-Liver-D1_002um_hires_image (Images), GSM9521683_Arc-Liver-D1_002um_square_002um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_008um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM9521683_Arc-Liver-D1_002um_downscaled_lowres', with elements:
        GSM9521683_Arc-Liver-D1_002um_lowres_image (Images), GSM9521683_Arc-Liver-D1_002um_square_002um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_008um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um (Shapes), GSM9521683_Arc-Liver-D1_002um_square_016um_for_vitessce (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("J1Dr8zbHMubB6OzG0000")
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("J1Dr8zbHMubB6OzG")   # 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 J1Dr8zbHMubB6OzG0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/J1Dr8zbHMubB6OzG

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid J1Dr8zbHMubB6OzG

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Inference of cell-cell communication in human fetal liver from high definition spatial profiling using Renoir→

2 datasets · publication

Metadata

Technology: Visium HD
Organism: human
Tissue: liver
Modality: RNA
Observations (bins): 333,667
Tier: bronze
Resolution: 5,302 × 6,000 px
mpp: 2.293 µm/px
Size: 672 MB
Sample ID: GSM9521683
License: NCBI GEO policy
Published: Mar 24, 2026

Cite this dataset

doi.org/10.1038/s41467-026-72388-7 ↗

BibTeX

@article{Rao_2026,
  title = {Charting spatial ligand-target activity using Renoir},
  volume = {17},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-026-72388-7},
  DOI = {10.1038/s41467-026-72388-7},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Rao, Narein and Kumar, Tanush and Kazemi, Dina and Hou, Shaozhi and Khakpoor, Atefeh and Eapen, Merrin Mary and Pai, Rhea and Qiao, Liang and Mishra, Archita and Ginhoux, Florent and Chan, Jerry Kok Yen and George, Jacob and Sharma, Ankur and Zafar, Hamim},
  year = {2026},
  month = May
}

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