Visium
Human prostate gland
human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard
silver Interactive viewer H&E prostate cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_full_image': DataTree[cyx] (3, 25188, 27472), (3, 12594, 13736), (3, 6297, 6868), (3, 3148, 3434), (3, 1574, 1717)
│ ├── 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_hires_image': DataArray[cyx] (3, 1834, 2000)
│ └── 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_lowres_image': DataArray[cyx] (3, 550, 600)
├── Shapes
│ └── 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma': GeoDataFrame shape: (3043, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3043, 17943)
with coordinate systems:
▸ 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma', with elements:
Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_full_image (Images), Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_hires_image (Images), Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_lowres_image (Images), Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma (Shapes)
▸ 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_downscaled_hires', with elements:
Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_hires_image (Images), Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma (Shapes)
▸ 'Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_downscaled_lowres', with elements:
Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma_lowres_image (Images), Visium_FFPE_Human_Prostate_Acinar_Cell_Carcinoma (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("pVubVQpxeBueBEvw0000")
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("pVubVQpxeBueBEvw") # 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 pVubVQpxeBueBEvw0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pVubVQpxeBueBEvw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pVubVQpxeBueBEvwLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- prostate cancer
- Modality
- RNA
- Observations (spots)
- 3,043
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 27,472 × 25,188 px
- mpp
- 0.291 µm/px
- Size
- 1.7 GB
- Sample ID
- human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard
- License
- CC BY 4.0
- Published
- Oct 8, 2021
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB