Visium

Mouse uterus

GSM8022509

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8022509_Day4_hires_image': DataArray[cyx] (3, 1855, 2000)
│     └── 'GSM8022509_Day4_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│     └── 'GSM8022509_Day4': GeoDataFrame shape: (296, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (296, 32285)
with coordinate systems:
    ▸ 'GSM8022509_Day4', with elements:
        GSM8022509_Day4_hires_image (Images), GSM8022509_Day4_lowres_image (Images), GSM8022509_Day4 (Shapes)
    ▸ 'GSM8022509_Day4_downscaled_hires', with elements:
        GSM8022509_Day4_hires_image (Images), GSM8022509_Day4 (Shapes)
    ▸ 'GSM8022509_Day4_downscaled_lowres', with elements:
        GSM8022509_Day4_lowres_image (Images), GSM8022509_Day4 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("n0E9xdiEFQpvspN60000")
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("n0E9xdiEFQpvspN6")   # 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 n0E9xdiEFQpvspN60000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/n0E9xdiEFQpvspN6

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid n0E9xdiEFQpvspN6

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Mouse uterine gene expressions during peri-implantation period→

3 datasets · other

Metadata

Technology: Visium
Organism: mouse
Tissue: uterus
Modality: RNA
Observations (spots): 296
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,855 px
mpp: 3.620 µm/px
Size: 9.9 MB
Sample ID: GSM8022509
License: NCBI GEO policy
Published: Oct 8, 2024

Cite this dataset

doi.org/10.1172/jci.insight.181865 ↗

BibTeX

@article{Aikawa_2024,
  title = {Spatiotemporally distinct roles of cyclooxygenase-1 and cyclooxygenase-2 at fetomaternal interface in mice},
  volume = {9},
  ISSN = {2379-3708},
  url = {http://dx.doi.org/10.1172/jci.insight.181865},
  DOI = {10.1172/jci.insight.181865},
  number = {19},
  journal = {JCI Insight},
  publisher = {American Society for Clinical Investigation},
  author = {Aikawa, Shizu and Matsuo, Mitsunori and Akaeda, Shun and Sugimoto, Yukihiko and Arita, Makoto and Isobe, Yosuke and Sugiura, Yuki and Taira, Shu and Maeda, Rae and Shimizu-Hirota, Ryoko and Takeda, Norihiko and Hiratsuka, Daiki and He, Xueting and Ishizawa, Chihiro and Iida, Rei and Fukui, Yamato and Hiraoka, Takehiro and Harada, Miyuki and Wada-Hiraike, Osamu and Osuga, Yutaka and Hirota, Yasushi},
  year = {2024},
  month = Aug
}

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