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Visium

Human ilium

GSM8618659

bronze Interactive viewer H&E Provisional
Human ilium preview
print(sdata) 
SpatialData object
├── Images
│     ├── 'GSM8618659_E53_03_29607_hires_image': DataArray[cyx] (3, 2000, 1998)
│     └── 'GSM8618659_E53_03_29607_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│     └── 'GSM8618659_E53_03_29607': GeoDataFrame shape: (159, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (159, 36601)
with coordinate systems:
    ▸ 'GSM8618659_E53_03_29607', with elements:
        GSM8618659_E53_03_29607_hires_image (Images), GSM8618659_E53_03_29607_lowres_image (Images), GSM8618659_E53_03_29607 (Shapes)
    ▸ 'GSM8618659_E53_03_29607_downscaled_hires', with elements:
        GSM8618659_E53_03_29607_hires_image (Images), GSM8618659_E53_03_29607 (Shapes)
    ▸ 'GSM8618659_E53_03_29607_downscaled_lowres', with elements:
        GSM8618659_E53_03_29607_lowres_image (Images), GSM8618659_E53_03_29607 (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("eR0PV3zKuzSH1e6Z0000")
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("eR0PV3zKuzSH1e6Z")   # 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 eR0PV3zKuzSH1e6Z0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/eR0PV3zKuzSH1e6Z

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid eR0PV3zKuzSH1e6Z
Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue
Part of collection
single-cell multiomics data for the developing human pelvic girdle [spatial]→
28 datasets · replicates

Metadata

Technology
Visium
Organism
human
Tissue
ilium
Modality
RNA
Observations (spots)
159
Tier
bronze
Chemistry
Visium v1
Magnification
other
Resolution
1,998 × 2,000 px
mpp
3.277 µm/px
Size
10.7 MB
Sample ID
GSM8618659
License
NCBI GEO policy
Published
Jul 4, 2025

Cite this dataset

doi.org/10.1038/s41586-025-09399-9 ↗
BibTeX 
@article{Senevirathne_2025,
  title = {The evolution of hominin bipedalism in two steps},
  volume = {645},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-025-09399-9},
  DOI = {10.1038/s41586-025-09399-9},
  number = {8082},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Senevirathne, Gayani and Fernandopulle, Serena C. and Richard, Daniel and Baumgart, Stephanie L. and Christensen, Anika Liv and Fabbri, Matteo and Höppner, Jakob and Jüppner, Harald and Li, Peishu and Bothe, Vivien and Fröbisch, Nadia and Simcock, Ian and Arthurs, Owen J. and Calder, Alistair and Freilich, Naomi and Nowlan, Niamh C. and Glass, Ian A. and Craft, April and Capellini, Terence D.},
  year = {2025},
  month = Aug,
  pages = {952–963}
}

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