Visium

Human ovary

GSM8292467

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'GSM8292467_C2_hires_image': DataArray[cyx] (3, 2000, 2000)
├── Shapes
│     └── 'GSM8292467_C2': GeoDataFrame shape: (5067, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (5067, 18085)
with coordinate systems:
    ▸ 'GSM8292467_C2', with elements:
        GSM8292467_C2_hires_image (Images), GSM8292467_C2 (Shapes)
    ▸ 'GSM8292467_C2_downscaled_hires', with elements:
        GSM8292467_C2_hires_image (Images), GSM8292467_C2 (Shapes)
    ▸ 'GSM8292467_C2_downscaled_lowres', with elements:
        GSM8292467_C2 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("vluJ9YlrjEn2uRVa0000")
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("vluJ9YlrjEn2uRVa")   # 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 vluJ9YlrjEn2uRVa0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/vluJ9YlrjEn2uRVa

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vluJ9YlrjEn2uRVa

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia [Spatial transcriptomics]→

6 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: ovary
Modality: RNA
Observations (spots): 5,067
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 2,000 px
mpp: 6.412 µm/px
Size: 103 MB
Sample ID: GSM8292467
License: NCBI GEO policy
Published: Feb 19, 2025

Cite this dataset

doi.org/10.1002/ctm2.70043 ↗

BibTeX

@article{Kavarthapu_2024,
  title = {Single‐nucleus and spatial transcriptomics of paediatric ovary: Molecular insights into the dysregulated signalling pathways underlying premature ovarian insufficiency in classic galactosemia},
  volume = {14},
  ISSN = {2001-1326},
  url = {http://dx.doi.org/10.1002/ctm2.70043},
  DOI = {10.1002/ctm2.70043},
  number = {10},
  journal = {Clinical and Translational Medicine},
  publisher = {Wiley},
  author = {Kavarthapu, Raghuveer and Lou, Hong and Pham, Thang and Do, Han and Soliman, Mary E. and Badger, Taylor and Balasubramanian, Ramya and Huyhn, Victoria and De La Luz Sierra, Maria and Yano Maher, Jacqueline C. and Gomez‐Lobo, Veronica},
  year = {2024},
  month = Oct
}

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