Visium
Mouse lung
mouse-tissue-microarray-in-3x3-layout-with-2-mm-edge-to-edge-spacing-ffpe-2-standard
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_full_image': DataTree[cyx] (3, 48839, 50834), (3, 24419, 25417), (3, 12209, 12708), (3, 6104, 6354), (3, 3052, 3177)
│ ├── 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_hires_image': DataArray[cyx] (3, 1922, 2000)
│ └── 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_lowres_image': DataArray[cyx] (3, 577, 600)
├── Shapes
│ └── 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm': GeoDataFrame shape: (4049, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4049, 19465)
with coordinate systems:
▸ 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm', with elements:
CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_full_image (Images), CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_hires_image (Images), CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_lowres_image (Images), CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm (Shapes)
▸ 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_downscaled_hires', with elements:
CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_hires_image (Images), CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm (Shapes)
▸ 'CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_downscaled_lowres', with elements:
CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_lowres_image (Images), CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("uZdsLxuaToqFC7ta0000")
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("uZdsLxuaToqFC7ta") # 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 uZdsLxuaToqFC7ta0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/uZdsLxuaToqFC7ta
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid uZdsLxuaToqFC7taLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Modality
- RNA
- Observations (spots)
- 4,049
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 50,834 × 48,839 px
- mpp
- 0.251 µm/px
- Size
- 4.6 GB
- Sample ID
- mouse-tissue-microarray-in-3x3-layout-with-2-mm-edge-to-edge-spacing-ffpe-2-standard
- License
- CC BY 4.0
- Published
- Feb 21, 2023
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