Visium
Human kidney
INT16
silver Interactive viewer H&E clear cell renal carcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'INT16_full_image': DataTree[cyx] (3, 16884, 17158), (3, 8442, 8579), (3, 4221, 4289), (3, 2110, 2144)
├── Shapes
│ └── 'INT16_spots': GeoDataFrame shape: (3206, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3206, 17943)
with coordinate systems:
▸ 'global', with elements:
INT16_full_image (Images), INT16_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("mpiM5bGXtUop5CDx0000")
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("mpiM5bGXtUop5CDx") # 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 mpiM5bGXtUop5CDx0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/mpiM5bGXtUop5CDx
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mpiM5bGXtUop5CDxLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer→ 24 datasets · replicates
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Condition
- clear cell renal carcinoma
- Modality
- RNA
- Observations (spots)
- 3,206
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 17,158 × 16,884 px
- mpp
- 0.458 µm/px
- Size
- 723 MB
- Sample ID
- INT16
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Mar 3, 2022
Cite this dataset
doi.org/10.1016/j.immuni.2022.02.001 ↗ BibTeX
@article{Meylan_2022,
title = {Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer},
volume = {55},
ISSN = {1074-7613},
url = {http://dx.doi.org/10.1016/j.immuni.2022.02.001},
DOI = {10.1016/j.immuni.2022.02.001},
number = {3},
journal = {Immunity},
publisher = {Elsevier BV},
author = {Meylan, Maxime and Petitprez, Florent and Becht, Etienne and Bougoüin, Antoine and Pupier, Guilhem and Calvez, Anne and Giglioli, Ilenia and Verkarre, Virginie and Lacroix, Guillaume and Verneau, Johanna and Sun, Chen-Ming and Laurent-Puig, Pierre and Vano, Yann-Alexandre and Elaïdi, Reza and Méjean, Arnaud and Sanchez-Salas, Rafaël and Barret, Eric and Cathelineau, Xavier and Oudard, Stephane and Reynaud, Claude-Agnès and de Reyniès, Aurélien and Sautès-Fridman, Catherine and Fridman, Wolf Herman},
year = {2022},
month = Mar,
pages = {527–541.e5}
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB