Visium
Human ovary
GSM8207502
silver Interactive viewer H&E ovarian serous adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'GSM8207502_CPS_OV5LtOV4_full_image': DataTree[cyx] (3, 2979, 3030), (3, 1489, 1515), (3, 744, 757), (3, 372, 378), (3, 186, 189)
├── Shapes
│ └── 'GSM8207502_CPS_OV5LtOV4': GeoDataFrame shape: (3623, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3623, 36601)
with coordinate systems:
▸ 'GSM8207502_CPS_OV5LtOV4', with elements:
GSM8207502_CPS_OV5LtOV4_full_image (Images), GSM8207502_CPS_OV5LtOV4 (Shapes)
▸ 'GSM8207502_CPS_OV5LtOV4_downscaled_hires', with elements:
GSM8207502_CPS_OV5LtOV4 (Shapes)
▸ 'GSM8207502_CPS_OV5LtOV4_downscaled_lowres', with elements:
GSM8207502_CPS_OV5LtOV4 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("BRxbcI2AhAgAtLpn0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("BRxbcI2AhAgAtLpn") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download BRxbcI2AhAgAtLpn0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/BRxbcI2AhAgAtLpn
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid BRxbcI2AhAgAtLpnLicense: NCBI GEO policy
Part of collection
Analysis of Spatial Transcriptomics for Unveiling the novel molecular characteristics of Recurrent and Non-Recurrent High-Grade Serous Ovarian Cancer→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- ovary
- Condition
- ovarian serous adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 3,623
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 3,030 × 2,979 px
- mpp
- 2.351 µm/px
- Size
- 60.6 MB
- Sample ID
- GSM8207502
- License
- NCBI GEO policy
- Published
- Apr 18, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB