Visium
Mouse kidney
NCBI596
silver Interactive viewer H&E bacterial infectious disease with sepsis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI596_full_image': DataTree[cyx] (3, 11297, 10468), (3, 5648, 5234), (3, 2824, 2617), (3, 1412, 1308)
├── Shapes
│ └── 'NCBI596_spots': GeoDataFrame shape: (1888, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1888, 31053)
with coordinate systems:
▸ 'global', with elements:
NCBI596_full_image (Images), NCBI596_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("WZSaovLCsJkiWF2c0000")
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("WZSaovLCsJkiWF2c") # 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 WZSaovLCsJkiWF2c0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WZSaovLCsJkiWF2c
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WZSaovLCsJkiWF2cLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury→ 3 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- kidney
- Condition
- bacterial infectious disease with sepsis
- Modality
- RNA
- Observations (spots)
- 1,888
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 10,468 × 11,297 px
- mpp
- 0.758 µm/px
- Size
- 253 MB
- Sample ID
- NCBI596
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jun 1, 2021
Cite this dataset
No linked publication found — please cite the data source.
License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB