Vizgen MERSCOPE
Mouse embryo
GSM7890129
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (6835, 2) (2D shapes)
└── Tables
└── 'table': AnnData (6835, 296)
with coordinate systems:
▸ 'global', with elements:
cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("1ikKi4QssrkRKSY80000")
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("1ikKi4QssrkRKSY8") # 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 1ikKi4QssrkRKSY80000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1ikKi4QssrkRKSY8
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1ikKi4QssrkRKSY8License: NCBI GEO policy
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- mouse
- Tissue
- embryo
- Modality
- RNA
- Observations (cells)
- 6,835
- Tier
- bronze
- Size
- 2.5 MB
- Sample ID
- GSM7890129
- License
- NCBI GEO policy
- Published
- Jan 25, 2024
Cite this dataset
doi.org/10.1161/CIRCRESAHA.123.323956 ↗ BibTeX
@article{geo:GSM7890129,
doi = {10.1161/CIRCRESAHA.123.323956},
title = {GSM7890129},
year = {2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB