Vizgen MERSCOPE
Human pleura
GSM9049386
bronze Interactive viewer pleural mesothelioma Provisional
print(sdata)
SpatialData object
├── Points
│ └── 'merscope_region_0_transcripts': DataFrame with shape: (35166439, 8) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (153981, 2) (2D shapes)
└── Tables
└── 'table': AnnData (153981, 500)
with coordinate systems:
▸ 'global', with elements:
merscope_region_0_transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("WgQtf06UzwGOg0W20000")
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("WgQtf06UzwGOg0W2") # 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 WgQtf06UzwGOg0W20000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WgQtf06UzwGOg0W2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WgQtf06UzwGOg0W2License: NCBI GEO policy
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- human
- Tissue
- pleura
- Condition
- pleural mesothelioma
- Modality
- RNA
- Observations (cells)
- 153,981
- Transcripts
- 35,166,439
- Tier
- bronze
- Size
- 788 MB
- Sample ID
- GSM9049386
- License
- NCBI GEO policy
- Published
- Jun 30, 2025
Cite this dataset
doi.org/10.1038/s41467-025-63414-1 ↗ BibTeX
@article{geo:GSM9049386,
doi = {10.1038/s41467-025-63414-1},
title = {GSM9049386},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB