Visium
Mouse brain
mouse-brain-coronal-section-2-ffpe-2-standard
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FFPE_Mouse_Brain_Rep2_full_image': DataTree[cyx] (3, 28062, 23735), (3, 14031, 11867), (3, 7015, 5933), (3, 3507, 2966), (3, 1753, 1483)
│ ├── 'CytAssist_FFPE_Mouse_Brain_Rep2_hires_image': DataArray[cyx] (3, 2000, 1692)
│ └── 'CytAssist_FFPE_Mouse_Brain_Rep2_lowres_image': DataArray[cyx] (3, 600, 508)
├── Shapes
│ └── 'CytAssist_FFPE_Mouse_Brain_Rep2': GeoDataFrame shape: (2235, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2235, 19465)
with coordinate systems:
▸ 'CytAssist_FFPE_Mouse_Brain_Rep2', with elements:
CytAssist_FFPE_Mouse_Brain_Rep2_full_image (Images), CytAssist_FFPE_Mouse_Brain_Rep2_hires_image (Images), CytAssist_FFPE_Mouse_Brain_Rep2_lowres_image (Images), CytAssist_FFPE_Mouse_Brain_Rep2 (Shapes)
▸ 'CytAssist_FFPE_Mouse_Brain_Rep2_downscaled_hires', with elements:
CytAssist_FFPE_Mouse_Brain_Rep2_hires_image (Images), CytAssist_FFPE_Mouse_Brain_Rep2 (Shapes)
▸ 'CytAssist_FFPE_Mouse_Brain_Rep2_downscaled_lowres', with elements:
CytAssist_FFPE_Mouse_Brain_Rep2_lowres_image (Images), CytAssist_FFPE_Mouse_Brain_Rep2 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("JevzoKUZbM722cqJ") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JevzoKUZbM722cqJ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JevzoKUZbM722cqJ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["JevzoKUZbM722cqJ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 2,235
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 23,735 × 28,062 px
- mpp
- 0.215 µm/px
- Size
- 1.3 GB
- Sample ID
- mouse-brain-coronal-section-2-ffpe-2-standard
- License
- CC BY 4.0
- Published
- Jul 13, 2022
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