Visium
Mouse kidney
adult-mouse-kidney-ffpe-1-standard-1-3-0
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_FFPE_Mouse_Kidney_full_image': DataTree[cyx] (4, 25260, 27443), (4, 12630, 13721), (4, 6315, 6860), (4, 3157, 3430), (4, 1578, 1715)
│ ├── 'Visium_FFPE_Mouse_Kidney_hires_image': DataArray[cyx] (3, 1841, 2000)
│ └── 'Visium_FFPE_Mouse_Kidney_lowres_image': DataArray[cyx] (3, 552, 600)
├── Shapes
│ └── 'Visium_FFPE_Mouse_Kidney': GeoDataFrame shape: (3124, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3124, 19465)
with coordinate systems:
▸ 'Visium_FFPE_Mouse_Kidney', with elements:
Visium_FFPE_Mouse_Kidney_full_image (Images), Visium_FFPE_Mouse_Kidney_hires_image (Images), Visium_FFPE_Mouse_Kidney_lowres_image (Images), Visium_FFPE_Mouse_Kidney (Shapes)
▸ 'Visium_FFPE_Mouse_Kidney_downscaled_hires', with elements:
Visium_FFPE_Mouse_Kidney_hires_image (Images), Visium_FFPE_Mouse_Kidney (Shapes)
▸ 'Visium_FFPE_Mouse_Kidney_downscaled_lowres', with elements:
Visium_FFPE_Mouse_Kidney_lowres_image (Images), Visium_FFPE_Mouse_Kidney (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("1C4Vb3fEtnXsDroX0000")
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("1C4Vb3fEtnXsDroX") # 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 1C4Vb3fEtnXsDroX0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1C4Vb3fEtnXsDroX
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1C4Vb3fEtnXsDroXLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- kidney
- Modality
- RNA
- Observations (spots)
- 3,124
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,841 px
- mpp
- 4.000 µm/px
- Size
- 1.8 GB
- Sample ID
- adult-mouse-kidney-ffpe-1-standard-1-3-0
- License
- CC BY 4.0
- Published
- Aug 16, 2021
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB