Vizgen MERSCOPE
Mouse brain
GSM8082301
silver Interactive viewer brain injury No linked publication
print(sdata)
SpatialData object
├── Points
│ └── 'merscope_region_0_transcripts': DataFrame with shape: (111814596, 8) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (1550129, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1550129, 496)
with coordinate systems:
▸ 'global', with elements:
merscope_region_0_transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("X9luiKFoElkNx12M0000")
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("X9luiKFoElkNx12M") # 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 X9luiKFoElkNx12M0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/X9luiKFoElkNx12M
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid X9luiKFoElkNx12MLicense: NCBI GEO policy
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- mouse
- Tissue
- brain
- Condition
- brain injury
- Modality
- RNA
- Observations (cells)
- 1,550,129
- Transcripts
- 111,814,596
- Tier
- silver
- Size
- 2.7 GB
- Sample ID
- GSM8082301
- License
- NCBI GEO policy
- Published
- Aug 1, 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