Visium
Human ovary
GSM8207500
silver Interactive viewer H&E ovarian serous adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'GSM8207500_CPS_OV34RtOV1_full_image': DataTree[cyx] (3, 3003, 2944), (3, 1501, 1472), (3, 750, 736), (3, 375, 368), (3, 187, 184)
├── Shapes
│ └── 'GSM8207500_CPS_OV34RtOV1': GeoDataFrame shape: (4274, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4274, 36601)
with coordinate systems:
▸ 'GSM8207500_CPS_OV34RtOV1', with elements:
GSM8207500_CPS_OV34RtOV1_full_image (Images), GSM8207500_CPS_OV34RtOV1 (Shapes)
▸ 'GSM8207500_CPS_OV34RtOV1_downscaled_hires', with elements:
GSM8207500_CPS_OV34RtOV1 (Shapes)
▸ 'GSM8207500_CPS_OV34RtOV1_downscaled_lowres', with elements:
GSM8207500_CPS_OV34RtOV1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("IRGrxigbE1epIXj50000")
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("IRGrxigbE1epIXj5") # 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 IRGrxigbE1epIXj50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/IRGrxigbE1epIXj5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid IRGrxigbE1epIXj5License: 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)
- 4,274
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,944 × 3,003 px
- mpp
- 2.230 µm/px
- Size
- 64.5 MB
- Sample ID
- GSM8207500
- 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