Vizgen MERSCOPE
Macaque basal ganglion
QM23.50.001.CX.46.04.09.02
silver Interactive viewer ✓ Verified publication
print(sdata)
SpatialData object
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (9, 2) (2D shapes)
└── Tables
└── 'table': AnnData (9, 300)
with coordinate systems:
▸ 'global', with elements:
cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("0yftzwYvxZpqll400000")
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("0yftzwYvxZpqll40") # 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 0yftzwYvxZpqll400000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/0yftzwYvxZpqll40
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0yftzwYvxZpqll40License: Allen Institute Terms of Use (noncommercial)
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- macaque
- Tissue
- basal ganglion
- Modality
- RNA
- Observations (cells)
- 9
- Tier
- silver
- Size
- 142 KB
- Sample ID
- QM23.50.001.CX.46.04.09.02
- License
- Allen Institute Terms of Use NonCommercial
- Published
- Jun 30, 2025
Cite this dataset
doi.org/10.1101/2025.11.22.688128 ↗ BibTeX
@article{Hewitt_2025,
title = {A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia},
url = {http://dx.doi.org/10.1101/2025.11.22.688128},
DOI = {10.1101/2025.11.22.688128},
publisher = {openRxiv},
author = {Hewitt, Madeleine N. and Turner, Meghan A. and Johansen, Nelson and McMillen, Delissa A. and Dan, Shu and DeBerardine, Mike and Ruiz, Augustin and Huang, Mike and Quon, Jacob and Fu, Yuanyuan and Kapen, Inkar and Barta, Stuard and Martin, Naomi and Cuevas, Nasmil Valera and Olsen, Paul and Nagra, Josh and Campos, Jazmin and VanNess, Marshall M. and Ransford, Shea and Juneau, Zoe and Hastings, Sam and Ching, Lindsey and Kunst, Michael and Basu, Soumyadeep and Höllt, Thomas and Li, Chang and Lelieveldt, Boudewijn and Yazdani, Faraz and Zhang, Qiangge and Levandowski, Kirsten and Feng, Guoping and Rosen, Burke Q. and Glasser, Matthew F. and Hayashi, Takuya and Garcia, Aaron D. and Kana, Omar and Maltzer, Zoe M. and Campagnola, Luke and Jarsky, Tim and Kruse, Lauren and Freiwald, Winrich and Keene, C. Dirk and Van Essen, David C. and Ariza, Jeanelle and Waters, Jack and Krienen, Fenna M. and Bakken, Trygve E. and Hodge, Rebecca D. and Ng, Lydia and Zeng, Hongkui and Lein, Ed S. and Close, Jennie L. and Long, Brian and Seeman, Stephanie C.},
year = {2025},
month = Nov
}Source: alleninstitute.github.io ↗ · License: Allen Institute Terms of Use ↗ · Reprocessed to SpatialData by SpatialData-DB