Visium
Mouse trunk
GSM4861204
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM4861204_Visium-C1_hires_image': DataArray[cyx] (3, 2000, 1997)
├── Shapes
│ └── 'GSM4861204_Visium-C1': GeoDataFrame shape: (192, 2) (2D shapes)
└── Tables
└── 'table': AnnData (192, 53574)
with coordinate systems:
▸ 'GSM4861204_Visium-C1', with elements:
GSM4861204_Visium-C1_hires_image (Images), GSM4861204_Visium-C1 (Shapes)
▸ 'GSM4861204_Visium-C1_downscaled_hires', with elements:
GSM4861204_Visium-C1_hires_image (Images), GSM4861204_Visium-C1 (Shapes)
▸ 'GSM4861204_Visium-C1_downscaled_lowres', with elements:
GSM4861204_Visium-C1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("EMS0unVubRENrRu8") # 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/EMS0unVubRENrRu8
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid EMS0unVubRENrRu8 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["EMS0unVubRENrRu80000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics]→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- trunk
- Modality
- RNA
- Observations
- 192
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,997 × 2,000 px
- mpp
- 3.552 µm/px
- Size
- 3.8 MB
- Sample ID
- GSM4861204
- License
- unknown
- Published
- Feb 16, 2021
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB