Visium HD
Mouse brain
visium-hd-cytassist-gene-expression-mouse-brain-fixed-frozen
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'Visium_HD_Mouse_Brain_Fixed_Frozen_full_image': DataTree[cyx] (3, 20667, 25808), (3, 10333, 12904), (3, 5166, 6452), (3, 2583, 3226), (3, 1291, 1613)
├── Shapes
│ ├── 'Visium_HD_Mouse_Brain_Fixed_Frozen_square_002um': GeoDataFrame shape: (6947755, 1) (2D shapes)
│ ├── 'Visium_HD_Mouse_Brain_Fixed_Frozen_square_008um': GeoDataFrame shape: (435605, 1) (2D shapes)
│ ├── 'Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um': GeoDataFrame shape: (109332, 1) (2D shapes)
│ └── 'Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um_for_vitessce': GeoDataFrame shape: (109332, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (6947755, 19059)
├── 'square_008um': AnnData (435605, 19059)
└── 'square_016um': AnnData (109332, 19059)
with coordinate systems:
▸ 'Visium_HD_Mouse_Brain_Fixed_Frozen', with elements:
Visium_HD_Mouse_Brain_Fixed_Frozen_full_image (Images), Visium_HD_Mouse_Brain_Fixed_Frozen_square_002um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_008um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Mouse_Brain_Fixed_Frozen_downscaled_hires', with elements:
Visium_HD_Mouse_Brain_Fixed_Frozen_square_002um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_008um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Mouse_Brain_Fixed_Frozen_downscaled_lowres', with elements:
Visium_HD_Mouse_Brain_Fixed_Frozen_square_002um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_008um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um (Shapes), Visium_HD_Mouse_Brain_Fixed_Frozen_square_016um_for_vitessce (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("URjHhR0P4lrqBPHe") # 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/URjHhR0P4lrqBPHe
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid URjHhR0P4lrqBPHe Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["URjHhR0P4lrqBPHe0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium HD
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 435,605
- Tier
- silver
- Chemistry
- Visium HD v1
- Magnification
- 40x
- Resolution
- 25,808 × 20,667 px
- mpp
- 0.274 µm/px
- Size
- 2.6 GB
- Sample ID
- visium-hd-cytassist-gene-expression-mouse-brain-fixed-frozen
- License
- CC BY 4.0
- Published
- Sep 17, 2024
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