Visium
Mouse brain
fixed-frozen-visium-on-cytassist-mouse-brain-probe-based-whole-transcriptome-profiling-2-standard
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_full_image': DataTree[cyx] (3, 46200, 34428), (3, 23100, 17214), (3, 11550, 8607), (3, 5775, 4303), (3, 2887, 2151)
│ ├── 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_hires_image': DataArray[cyx] (3, 2000, 1491)
│ └── 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_lowres_image': DataArray[cyx] (3, 600, 447)
├── Shapes
│ └── 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain': GeoDataFrame shape: (5123, 2) (2D shapes)
└── Tables
└── 'table': AnnData (5123, 19465)
with coordinate systems:
▸ 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain', with elements:
CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_full_image (Images), CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_hires_image (Images), CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_lowres_image (Images), CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain (Shapes)
▸ 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_downscaled_hires', with elements:
CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_hires_image (Images), CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain (Shapes)
▸ 'CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_downscaled_lowres', with elements:
CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain_lowres_image (Images), CytAssist_Fixed_Frozen_Sagittal_Mouse_Brain (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("9NhlWy8kI2wYlhPz0000")
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("9NhlWy8kI2wYlhPz") # 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 9NhlWy8kI2wYlhPz0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9NhlWy8kI2wYlhPz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9NhlWy8kI2wYlhPzLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 5,123
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 34,428 × 46,200 px
- mpp
- 0.251 µm/px
- Size
- 3.6 GB
- Sample ID
- fixed-frozen-visium-on-cytassist-mouse-brain-probe-based-whole-transcriptome-profiling-2-standard
- License
- CC BY 4.0
- Published
- Apr 17, 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