Visium

Human prepuce of penis

GSM6806993

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'GSM6806993_D1_st_s2_hires_image': DataArray[cyx] (3, 1993, 2000)
├── Shapes
│     └── 'GSM6806993_D1_st_s2': GeoDataFrame shape: (653, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (653, 17943)
with coordinate systems:
    ▸ 'GSM6806993_D1_st_s2', with elements:
        GSM6806993_D1_st_s2_hires_image (Images), GSM6806993_D1_st_s2 (Shapes)
    ▸ 'GSM6806993_D1_st_s2_downscaled_hires', with elements:
        GSM6806993_D1_st_s2_hires_image (Images), GSM6806993_D1_st_s2 (Shapes)
    ▸ 'GSM6806993_D1_st_s2_downscaled_lowres', with elements:
        GSM6806993_D1_st_s2 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("E9eagK7oSNBeto8V0000")
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("E9eagK7oSNBeto8V")   # 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 E9eagK7oSNBeto8V0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/E9eagK7oSNBeto8V

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid E9eagK7oSNBeto8V

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]→

2 datasets · other

Metadata

Technology: Visium
Organism: human
Tissue: prepuce of penis
Modality: RNA
Observations (spots): 653
Tier: bronze
Chemistry: Visium v1
Resolution: 2,000 × 1,993 px
mpp: 4.211 µm/px
Size: 13.5 MB
Sample ID: GSM6806993
License: NCBI GEO policy
Published: Aug 8, 2023

Cite this dataset

doi.org/10.1101/2023.01.04.522502 ↗

BibTeX

@article{geo:GSM6806993,
  doi = {10.1101/2023.01.04.522502},
  title = {GSM6806993},
  year = {2023}
}

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