Visium
Mouse brain
ffpe-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_FFPE_Sagittal_Mouse_Brain_full_image': DataTree[cyx] (3, 48372, 45106), (3, 24186, 22553), (3, 12093, 11276), (3, 6046, 5638), (3, 3023, 2819)
│ ├── 'CytAssist_FFPE_Sagittal_Mouse_Brain_hires_image': DataArray[cyx] (3, 2000, 1865)
│ └── 'CytAssist_FFPE_Sagittal_Mouse_Brain_lowres_image': DataArray[cyx] (3, 600, 560)
├── Shapes
│ └── 'CytAssist_FFPE_Sagittal_Mouse_Brain': GeoDataFrame shape: (8462, 2) (2D shapes)
└── Tables
└── 'table': AnnData (8462, 19465)
with coordinate systems:
▸ 'CytAssist_FFPE_Sagittal_Mouse_Brain', with elements:
CytAssist_FFPE_Sagittal_Mouse_Brain_full_image (Images), CytAssist_FFPE_Sagittal_Mouse_Brain_hires_image (Images), CytAssist_FFPE_Sagittal_Mouse_Brain_lowres_image (Images), CytAssist_FFPE_Sagittal_Mouse_Brain (Shapes)
▸ 'CytAssist_FFPE_Sagittal_Mouse_Brain_downscaled_hires', with elements:
CytAssist_FFPE_Sagittal_Mouse_Brain_hires_image (Images), CytAssist_FFPE_Sagittal_Mouse_Brain (Shapes)
▸ 'CytAssist_FFPE_Sagittal_Mouse_Brain_downscaled_lowres', with elements:
CytAssist_FFPE_Sagittal_Mouse_Brain_lowres_image (Images), CytAssist_FFPE_Sagittal_Mouse_Brain (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("3BkzLifriuCYpVAa") # 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/3BkzLifriuCYpVAa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3BkzLifriuCYpVAa Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3BkzLifriuCYpVAa0000"])[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
- 8,462
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 45,106 × 48,372 px
- mpp
- 0.251 µm/px
- Size
- 4.2 GB
- Sample ID
- ffpe-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