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Visium

Human prostate gland

GSE230282

bronze Interactive viewer H&E prostate cancer Provisional
Human prostate gland preview
print(sdata) 
SpatialData object
├── Images
│     └── 'GSM7211257_EHU-W3_hires_image': DataArray[cyx] (3, 1501, 2000)
├── Shapes
│     └── 'GSM7211257_EHU-W3': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 37082)
with coordinate systems:
    ▸ 'GSM7211257_EHU-W3', with elements:
        GSM7211257_EHU-W3_hires_image (Images), GSM7211257_EHU-W3 (Shapes)
    ▸ 'GSM7211257_EHU-W3_downscaled_hires', with elements:
        GSM7211257_EHU-W3_hires_image (Images), GSM7211257_EHU-W3 (Shapes)
    ▸ 'GSM7211257_EHU-W3_downscaled_lowres', with elements:
        GSM7211257_EHU-W3 (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("G2Dau41bre59E2Gd0000")
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("G2Dau41bre59E2Gd")   # 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 G2Dau41bre59E2Gd0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/G2Dau41bre59E2Gd

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid G2Dau41bre59E2Gd
Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Metadata

Technology
Visium
Organism
human
Tissue
prostate gland
Condition
prostate cancer
Modality
RNA
Observations (spots)
4,992
Tier
bronze
Chemistry
Visium v1
Resolution
2,000 × 1,501 px
mpp
5.387 µm/px
Size
129 MB
Sample ID
GSE230282
License
NCBI GEO policy
Published
May 17, 2023

Cite this dataset

doi.org/10.3390/ijms24108955 ↗
BibTeX 
@article{geo:GSE230282,
  doi = {10.3390/ijms24108955},
  title = {GSE230282},
  year = {2023}
}

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