Visium
Mouse olfactory bulb
adult-mouse-olfactory-bulb-1-standard-1
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_Mouse_Olfactory_Bulb_full_image': DataTree[cyx] (4, 10000, 10000), (4, 5000, 5000), (4, 2500, 2500), (4, 1250, 1250), (4, 625, 625)
│ ├── 'Visium_Mouse_Olfactory_Bulb_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'Visium_Mouse_Olfactory_Bulb_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'Visium_Mouse_Olfactory_Bulb': GeoDataFrame shape: (1185, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1185, 32285)
with coordinate systems:
▸ 'Visium_Mouse_Olfactory_Bulb', with elements:
Visium_Mouse_Olfactory_Bulb_full_image (Images), Visium_Mouse_Olfactory_Bulb_hires_image (Images), Visium_Mouse_Olfactory_Bulb_lowres_image (Images), Visium_Mouse_Olfactory_Bulb (Shapes)
▸ 'Visium_Mouse_Olfactory_Bulb_downscaled_hires', with elements:
Visium_Mouse_Olfactory_Bulb_hires_image (Images), Visium_Mouse_Olfactory_Bulb (Shapes)
▸ 'Visium_Mouse_Olfactory_Bulb_downscaled_lowres', with elements:
Visium_Mouse_Olfactory_Bulb_lowres_image (Images), Visium_Mouse_Olfactory_Bulb (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("67V03BYH1oHZPtgc0000")
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("67V03BYH1oHZPtgc") # 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 67V03BYH1oHZPtgc0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/67V03BYH1oHZPtgc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 67V03BYH1oHZPtgcLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- olfactory bulb
- Modality
- RNA
- Observations (spots)
- 1,185
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.736 µm/px
- Size
- 163 MB
- Sample ID
- adult-mouse-olfactory-bulb-1-standard-1
- License
- CC BY 4.0
- Published
- Jul 12, 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