Visium
Human prostate gland
human-prostate-cancer-adjacent-normal-section-with-if-staining-ffpe-1-standard
silver Interactive viewer H&E prostate adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_FFPE_Human_Prostate_IF_full_image': DataTree[cyx] (3, 25088, 26624), (3, 12544, 13312), (3, 6272, 6656), (3, 3136, 3328), (3, 1568, 1664)
│ ├── 'Visium_FFPE_Human_Prostate_IF_hires_image': DataArray[cyx] (3, 1885, 2000)
│ └── 'Visium_FFPE_Human_Prostate_IF_lowres_image': DataArray[cyx] (3, 566, 600)
├── Shapes
│ └── 'Visium_FFPE_Human_Prostate_IF': GeoDataFrame shape: (3460, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3460, 17943)
with coordinate systems:
▸ 'Visium_FFPE_Human_Prostate_IF', with elements:
Visium_FFPE_Human_Prostate_IF_full_image (Images), Visium_FFPE_Human_Prostate_IF_hires_image (Images), Visium_FFPE_Human_Prostate_IF_lowres_image (Images), Visium_FFPE_Human_Prostate_IF (Shapes)
▸ 'Visium_FFPE_Human_Prostate_IF_downscaled_hires', with elements:
Visium_FFPE_Human_Prostate_IF_hires_image (Images), Visium_FFPE_Human_Prostate_IF (Shapes)
▸ 'Visium_FFPE_Human_Prostate_IF_downscaled_lowres', with elements:
Visium_FFPE_Human_Prostate_IF_lowres_image (Images), Visium_FFPE_Human_Prostate_IF (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("QmJuR1aR0ZP61Hif0000")
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("QmJuR1aR0ZP61Hif") # 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 QmJuR1aR0ZP61Hif0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/QmJuR1aR0ZP61Hif
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid QmJuR1aR0ZP61HifLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- prostate adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 3,460
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 26,624 × 25,088 px
- mpp
- 0.292 µm/px
- Size
- 968 MB
- Sample ID
- human-prostate-cancer-adjacent-normal-section-with-if-staining-ffpe-1-standard
- License
- CC BY 4.0
- Published
- Jul 12, 2022
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