Visium

Human ovary

GSM7019836

bronze Interactive viewer H&E ovarian clear cell adenocarcinoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'GSM7019836_OCCS3v_hires_image': DataArray[cyx] (3, 1970, 2000)
├── Shapes
│     └── 'GSM7019836_OCCS3v': GeoDataFrame shape: (898, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (898, 36601)
with coordinate systems:
    ▸ 'GSM7019836_OCCS3v', with elements:
        GSM7019836_OCCS3v_hires_image (Images), GSM7019836_OCCS3v (Shapes)
    ▸ 'GSM7019836_OCCS3v_downscaled_hires', with elements:
        GSM7019836_OCCS3v_hires_image (Images), GSM7019836_OCCS3v (Shapes)
    ▸ 'GSM7019836_OCCS3v_downscaled_lowres', with elements:
        GSM7019836_OCCS3v (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("rDLvaIERUPPB37sy0000")
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("rDLvaIERUPPB37sy")   # 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 rDLvaIERUPPB37sy0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/rDLvaIERUPPB37sy

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rDLvaIERUPPB37sy

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]→

2 datasets · other

Metadata

Technology: Visium
Organism: human
Tissue: ovary
Condition: ovarian clear cell adenocarcinoma
Modality: RNA
Observations (spots): 898
Tier: bronze
Chemistry: Visium v1
Resolution: 2,000 × 1,970 px
mpp: 3.417 µm/px
Size: 14.9 MB
Sample ID: GSM7019836
License: NCBI GEO policy
Published: Mar 30, 2024

Cite this dataset

doi.org/10.1016/j.xcrm.2024.101532 ↗

BibTeX

@article{Mori_2024,
  title = {Targeting PDGF signaling of cancer-associated fibroblasts blocks feedback activation of HIF-1α and tumor progression of clear cell ovarian cancer},
  volume = {5},
  ISSN = {2666-3791},
  url = {http://dx.doi.org/10.1016/j.xcrm.2024.101532},
  DOI = {10.1016/j.xcrm.2024.101532},
  number = {5},
  journal = {Cell Reports Medicine},
  publisher = {Elsevier BV},
  author = {Mori, Yutaro and Okimoto, Yoshie and Sakai, Hiroaki and Kanda, Yusuke and Ohata, Hirokazu and Shiokawa, Daisuke and Suzuki, Mikiko and Yoshida, Hiroshi and Ueda, Haruka and Sekizuka, Tomoyuki and Tamura, Ryo and Yamawaki, Kaoru and Ishiguro, Tatsuya and Mateos, Raul Nicolas and Shiraishi, Yuichi and Yatabe, Yasushi and Hamada, Akinobu and Yoshihara, Kosuke and Enomoto, Takayuki and Okamoto, Koji},
  year = {2024},
  month = May,
  pages = {101532}
}

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