Visium
Human brain
GSM7596590
bronze Interactive viewer H&E glioblastoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM7596590_zh916bulk_lowres_image': DataArray[cyx] (3, 600, 586)
├── Shapes
│ └── 'GSM7596590_zh916bulk': GeoDataFrame shape: (2199, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2199, 33538)
with coordinate systems:
▸ 'GSM7596590_zh916bulk', with elements:
GSM7596590_zh916bulk_lowres_image (Images), GSM7596590_zh916bulk (Shapes)
▸ 'GSM7596590_zh916bulk_downscaled_hires', with elements:
GSM7596590_zh916bulk (Shapes)
▸ 'GSM7596590_zh916bulk_downscaled_lowres', with elements:
GSM7596590_zh916bulk_lowres_image (Images), GSM7596590_zh916bulk (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("xf3SZvH6Qn1fZTOK") # 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/xf3SZvH6Qn1fZTOK
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xf3SZvH6Qn1fZTOK Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["xf3SZvH6Qn1fZTOK0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Integrative spatial analysis reveals a multi-layered organization of glioblastoma→ 19 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- glioblastoma
- Modality
- RNA
- Observations
- 2,199
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 586 × 600 px
- mpp
- 12.710 µm/px
- Size
- 26 MB
- Sample ID
- GSM7596590
- License
- unknown
- Published
- Feb 18, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB