Visium
Mouse prostate gland
NCBI793
silver Interactive viewer H&E prostate adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI793_full_image': DataTree[cyx] (3, 9984, 10080), (3, 4992, 5040), (3, 2496, 2520), (3, 1248, 1260)
├── Shapes
│ └── 'NCBI793_spots': GeoDataFrame shape: (14110, 2) (2D shapes)
└── Tables
└── 'table': AnnData (14110, 32589)
with coordinate systems:
▸ 'global', with elements:
NCBI793_full_image (Images), NCBI793_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yD2xClzt7kmsM2nr0000")
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("yD2xClzt7kmsM2nr") # 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 yD2xClzt7kmsM2nr0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yD2xClzt7kmsM2nr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yD2xClzt7kmsM2nrLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Distinct mesenchymal cell states mediate prostate cancer progression [Spatial Transcriptomics]→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- prostate gland
- Condition
- prostate adenocarcinoma
- Modality
- RNA
- Observations (spots)
- 14,110
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 10,080 × 9,984 px
- mpp
- 0.901 µm/px
- Size
- 379 MB
- Sample ID
- NCBI793
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 1, 2023
Cite this dataset
doi.org/10.1101/2023.03.29.534769 ↗ BibTeX
@article{Pakula_2023,
title = {Distinct mesenchymal cell states mediate prostate cancer progression},
url = {http://dx.doi.org/10.1101/2023.03.29.534769},
DOI = {10.1101/2023.03.29.534769},
publisher = {openRxiv},
author = {Pakula, Hubert and Omar, Mohamed and Carelli, Ryan and Pederzoli, Filippo and Fanelli, Giuseppe Nicolò and Pannellini, Tania and Van Emmenis, Lucie and Rodrigues, Silvia and Fidalgo-Ribeiro, Caroline and Nuzzo, Pier V. and Brady, Nicholas J. and Jere, Madhavi and Unkenholz, Caitlin and Alexanderani, Mohammad K. and Khani, Francesca and de Almeida, Francisca Nunes and Abate-Shen, Cory and Greenblatt, Matthew B and Rickman, David S. and Barbieri, Christopher E. and Robinson, Brian D. and Marchionni, Luigi and Loda, Massimo},
year = {2023},
month = Apr
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB