Visium
Mouse prostate gland
GSM8686968
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8686968_slide3C_hires_image': DataArray[cyx] (3, 2000, 1951)
│ └── 'GSM8686968_slide3C_lowres_image': DataArray[cyx] (3, 600, 585)
├── Shapes
│ └── 'GSM8686968_slide3C': GeoDataFrame shape: (2481, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2481, 19465)
with coordinate systems:
▸ 'GSM8686968_slide3C', with elements:
GSM8686968_slide3C_hires_image (Images), GSM8686968_slide3C_lowres_image (Images), GSM8686968_slide3C (Shapes)
▸ 'GSM8686968_slide3C_downscaled_hires', with elements:
GSM8686968_slide3C_hires_image (Images), GSM8686968_slide3C (Shapes)
▸ 'GSM8686968_slide3C_downscaled_lowres', with elements:
GSM8686968_slide3C_lowres_image (Images), GSM8686968_slide3C (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Ehi3eVP4oDV5YwGH0000")
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("Ehi3eVP4oDV5YwGH") # 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 Ehi3eVP4oDV5YwGH0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Ehi3eVP4oDV5YwGH
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Ehi3eVP4oDV5YwGHLicense: NCBI GEO policy
Part of collection
Cellular cartography reveals mouse prostate organization and determinants of castration resistance [Spatial Transcriptomics]→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- prostate gland
- Modality
- RNA
- Observations (spots)
- 2,481
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,951 × 2,000 px
- mpp
- 4.122 µm/px
- Size
- 49.1 MB
- Sample ID
- GSM8686968
- License
- NCBI GEO policy
- Published
- Jan 15, 2025
Cite this dataset
doi.org/10.1101/2024.12.27.630532 ↗ BibTeX
@article{Cho_2024,
title = {Cellular cartography reveals mouse prostate organization and determinants of castration resistance},
url = {http://dx.doi.org/10.1101/2024.12.27.630532},
DOI = {10.1101/2024.12.27.630532},
publisher = {openRxiv},
author = {Cho, Hanbyul and Zhang, Yuping and Tien, Jean C. and Mannan, Rahul and Luo, Jie and Narayanan, Sathiya Pandi and Mahapatra, Somnath and Hu, Jing and Shelley, Greg and Cruz, Gabriel and Shahine, Miriam and Wang, Lisha and Su, Fengyun and Wang, Rui and Cao, Xuhong and Dhanasekaran, Saravana Mohan and Keller, Evan T. and Pitchiaya, Sethuramasundaram and Chinnaiyan, Arul M.},
year = {2024},
month = Dec
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB