Visium
Human urinary bladder
NCBI600
silver Interactive viewer H&E bladder transitional cell carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI600_full_image': DataTree[cyx] (3, 16208, 17170), (3, 8104, 8585), (3, 4052, 4292), (3, 2026, 2146)
├── Shapes
│ └── 'NCBI600_spots': GeoDataFrame shape: (832, 2) (2D shapes)
└── Tables
└── 'table': AnnData (832, 33538)
with coordinate systems:
▸ 'global', with elements:
NCBI600_full_image (Images), NCBI600_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("TwmOKMgANtJW9bUR0000")
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("TwmOKMgANtJW9bUR") # 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 TwmOKMgANtJW9bUR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/TwmOKMgANtJW9bUR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid TwmOKMgANtJW9bURLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
A new epithelial cell subpopulation predicts response to surgery, chemotherapy, and immunotherapy in bladder cancer→ 4 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- urinary bladder
- Condition
- bladder transitional cell carcinoma
- Modality
- RNA
- Observations (spots)
- 832
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 17,170 × 16,208 px
- mpp
- 0.488 µm/px
- Size
- 300 MB
- Sample ID
- NCBI600
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jun 4, 2021
Cite this dataset
No linked publication found — please cite the data source.
License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB