Visium
Human prostate gland
GSM8557979
bronze Interactive viewer H&E benign prostatic hyperplasia Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8557979_BPH_4_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM8557979_BPH_4_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM8557979_BPH_4': GeoDataFrame shape: (3841, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3841, 33538)
with coordinate systems:
▸ 'GSM8557979_BPH_4', with elements:
GSM8557979_BPH_4_hires_image (Images), GSM8557979_BPH_4_lowres_image (Images), GSM8557979_BPH_4 (Shapes)
▸ 'GSM8557979_BPH_4_downscaled_hires', with elements:
GSM8557979_BPH_4_hires_image (Images), GSM8557979_BPH_4 (Shapes)
▸ 'GSM8557979_BPH_4_downscaled_lowres', with elements:
GSM8557979_BPH_4_lowres_image (Images), GSM8557979_BPH_4 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("H6Iz5rdFX2EARcwr") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/H6Iz5rdFX2EARcwr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid H6Iz5rdFX2EARcwr Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["H6Iz5rdFX2EARcwr0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer→ 52 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- benign prostatic hyperplasia
- Modality
- RNA
- Observations
- 3,841
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 2,000 px
- mpp
- 4.017 µm/px
- Size
- 50 MB
- Sample ID
- GSM8557979
- License
- unknown
- Published
- Oct 29, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB