Visium
Human prostate gland
GSM8558008
bronze Interactive viewer H&E prostate cancer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8558008_NEADT_12_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM8558008_NEADT_12_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM8558008_NEADT_12': GeoDataFrame shape: (2296, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2296, 36601)
with coordinate systems:
▸ 'GSM8558008_NEADT_12', with elements:
GSM8558008_NEADT_12_hires_image (Images), GSM8558008_NEADT_12_lowres_image (Images), GSM8558008_NEADT_12 (Shapes)
▸ 'GSM8558008_NEADT_12_downscaled_hires', with elements:
GSM8558008_NEADT_12_hires_image (Images), GSM8558008_NEADT_12 (Shapes)
▸ 'GSM8558008_NEADT_12_downscaled_lowres', with elements:
GSM8558008_NEADT_12_lowres_image (Images), GSM8558008_NEADT_12 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("kc3SfDumg7ED1Ke30000")
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("kc3SfDumg7ED1Ke3") # 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 kc3SfDumg7ED1Ke30000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kc3SfDumg7ED1Ke3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kc3SfDumg7ED1Ke3License: NCBI GEO policy
Part of collection
Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer→ 52 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- prostate cancer
- Modality
- RNA
- Observations (spots)
- 2,296
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 4.059 µm/px
- Size
- 24.5 MB
- Sample ID
- GSM8558008
- License
- NCBI GEO policy
- Published
- Oct 29, 2024
Cite this dataset
doi.org/10.1038/s41467-024-54364-1 ↗ BibTeX
@article{Kiviaho_2024,
title = {Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-54364-1},
DOI = {10.1038/s41467-024-54364-1},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Kiviaho, Antti and Eerola, Sini K. and Kallio, Heini M. L. and Andersen, Maria K. and Hoikka, Miina and Tiihonen, Aliisa M. and Salonen, Iida and Spotbeen, Xander and Giesen, Alexander and Parker, Charles T. A. and Taavitsainen, Sinja and Hantula, Olli and Marttinen, Mikael and Hermelo, Ismaïl and Ismail, Mazlina and Midtbust, Elise and Wess, Maximilian and Devlies, Wout and Sharma, Abhibhav and Krossa, Sebastian and Häkkinen, Tomi and Afyounian, Ebrahim and Vandereyken, Katy and Kint, Sam and Kesseli, Juha and Tolonen, Teemu and Tammela, Teuvo L. J. and Viset, Trond and Størkersen, Øystein and Giskeødegård, Guro F. and Rye, Morten B. and Murtola, Teemu and Erickson, Andrew and Latonen, Leena and Bova, G. Steven and Mills, Ian G. and Joniau, Steven and Swinnen, Johannes V. and Voet, Thierry and Mirtti, Tuomas and Attard, Gerhardt and Claessens, Frank and Visakorpi, Tapio and Rautajoki, Kirsi J. and Tessem, May-Britt and Urbanucci, Alfonso and Nykter, Matti},
year = {2024},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB