Visium
Mouse gastrocnemius
GSM6996264
silver Interactive viewer H&E Duchenne muscular dystrophy No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_hires_image': DataArray[cyx] (3, 2000, 1972)
│ └── 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_lowres_image': DataArray[cyx] (3, 600, 592)
├── Shapes
│ └── 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2': GeoDataFrame shape: (814, 2) (2D shapes)
└── Tables
└── 'table': AnnData (814, 32285)
with coordinate systems:
▸ 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2', with elements:
GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_hires_image (Images), GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_lowres_image (Images), GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2 (Shapes)
▸ 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_downscaled_hires', with elements:
GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_hires_image (Images), GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2 (Shapes)
▸ 'GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_downscaled_lowres', with elements:
GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2_lowres_image (Images), GSM6996264_MDX_2mo_GAST_Pred_QW_Rep2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("f9mMP899QmtaZUn50000")
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("f9mMP899QmtaZUn5") # 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 f9mMP899QmtaZUn50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/f9mMP899QmtaZUn5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid f9mMP899QmtaZUn5License: NCBI GEO policy
Part of collection
Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture→ 7 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- gastrocnemius
- Condition
- Duchenne muscular dystrophy
- Modality
- RNA
- Observations (spots)
- 814
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,972 × 2,000 px
- mpp
- 3.376 µm/px
- Size
- 15.2 MB
- Sample ID
- GSM6996264
- License
- NCBI GEO policy
- Published
- Aug 28, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB