Vizgen MERSCOPE
Mouse brain
GSM6125921
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Points
│ └── 'merscope_region_0_transcripts': DataFrame with shape: (114018446, 8) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (126858, 2) (2D shapes)
└── Tables
└── 'table': AnnData (126858, 287)
with coordinate systems:
▸ 'global', with elements:
merscope_region_0_transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("AVvK8XFwnCWr5UNR0000")
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("AVvK8XFwnCWr5UNR") # 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 AVvK8XFwnCWr5UNR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/AVvK8XFwnCWr5UNR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AVvK8XFwnCWr5UNRLicense: NCBI GEO policy
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 126,858
- Transcripts
- 114,018,446
- Tier
- bronze
- Size
- 2.4 GB
- Sample ID
- GSM6125921
- License
- NCBI GEO policy
- Published
- Jun 21, 2023
Cite this dataset
doi.org/10.1038/s41467-023-39447-9 ↗ BibTeX
@article{geo:GSM6125921,
doi = {10.1038/s41467-023-39447-9},
title = {GSM6125921},
year = {2023}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB