Visium

Human ovary

GSM9241521

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'GSM9241521_C4_hires_image': DataArray[cyx] (3, 3000, 3000)
├── Shapes
│     └── 'GSM9241521_C4': GeoDataFrame shape: (1785, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1785, 18085)
with coordinate systems:
    ▸ 'GSM9241521_C4', with elements:
        GSM9241521_C4_hires_image (Images), GSM9241521_C4 (Shapes)
    ▸ 'GSM9241521_C4_downscaled_hires', with elements:
        GSM9241521_C4_hires_image (Images), GSM9241521_C4 (Shapes)
    ▸ 'GSM9241521_C4_downscaled_lowres', with elements:
        GSM9241521_C4 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("2AMm0At7sHgoMk5M0000")
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("2AMm0At7sHgoMk5M")   # 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 2AMm0At7sHgoMk5M0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/2AMm0At7sHgoMk5M

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 2AMm0At7sHgoMk5M

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Integrated single-cell and spatial transcriptomics of ovarian immune landscape reveal role of distinct macrophages in classic galactosemia associated with premature ovarian insufficiency→

2 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: ovary
Modality: RNA
Observations (spots): 1,785
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 3,000 × 3,000 px
mpp: 4.276 µm/px
Size: 68.9 MB
Sample ID: GSM9241521
License: NCBI GEO policy
Published: Aug 12, 2026

Cite this dataset

doi.org/10.1186/s12964-026-02950-9 ↗

BibTeX

@article{Kavarthapu_2026,
  title = {Transcriptomic profiling of the ovarian immune landscape reveals distinct macrophage subsets and activation of the NLRP3 inflammasome likely contributing to accelerated follicular atresia in classic galactosemia},
  volume = {24},
  ISSN = {1478-811X},
  url = {http://dx.doi.org/10.1186/s12964-026-02950-9},
  DOI = {10.1186/s12964-026-02950-9},
  number = {1},
  journal = {Cell Communication and Signaling},
  publisher = {Springer Science and Business Media LLC},
  author = {Kavarthapu, Raghuveer and Vo, Son and Hanby, Natalie and Vanpouille, Christophe and Brunette, Margaret and Soliman, Mary E and Pham, Thang and Lou, Hong and Sierra, Maria DeLa Luz and Maher, Jacqueline C Yano and Gomez-Lobo, Veronica},
  year = {2026},
  month = May
}

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