Vizgen MERSCOPE
Mouse brain
C57BL6J-638850.35
silver Interactive viewer ✓ Verified publication
print(sdata)
SpatialData object
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (87352, 2) (2D shapes)
└── Tables
└── 'table': AnnData (87352, 500)
with coordinate systems:
▸ 'global', with elements:
cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("FO7zwDQFKx7pRJ3p0000")
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("FO7zwDQFKx7pRJ3p") # 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 FO7zwDQFKx7pRJ3p0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/FO7zwDQFKx7pRJ3p
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FO7zwDQFKx7pRJ3pLicense: Allen Institute Terms of Use (noncommercial)
Metadata
- Technology
- Vizgen MERSCOPE
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 87,352
- Tier
- silver
- Size
- 59.5 MB
- Sample ID
- C57BL6J-638850.35
- License
- Allen Institute Terms of Use NonCommercial
- Published
- Dec 13, 2023
Cite this dataset
doi.org/10.1038/s41586-023-06812-z ↗ BibTeX
@article{Yao_2023,
title = {A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain},
volume = {624},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-023-06812-z},
DOI = {10.1038/s41586-023-06812-z},
number = {7991},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Yao, Zizhen and van Velthoven, Cindy T. J. and Kunst, Michael and Zhang, Meng and McMillen, Delissa and Lee, Changkyu and Jung, Won and Goldy, Jeff and Abdelhak, Aliya and Aitken, Matthew and Baker, Katherine and Baker, Pamela and Barkan, Eliza and Bertagnolli, Darren and Bhandiwad, Ashwin and Bielstein, Cameron and Bishwakarma, Prajal and Campos, Jazmin and Carey, Daniel and Casper, Tamara and Chakka, Anish Bhaswanth and Chakrabarty, Rushil and Chavan, Sakshi and Chen, Min and Clark, Michael and Close, Jennie and Crichton, Kirsten and Daniel, Scott and DiValentin, Peter and Dolbeare, Tim and Ellingwood, Lauren and Fiabane, Elysha and Fliss, Timothy and Gee, James and Gerstenberger, James and Glandon, Alexandra and Gloe, Jessica and Gould, Joshua and Gray, James and Guilford, Nathan and Guzman, Junitta and Hirschstein, Daniel and Ho, Windy and Hooper, Marcus and Huang, Mike and Hupp, Madie and Jin, Kelly and Kroll, Matthew and Lathia, Kanan and Leon, Arielle and Li, Su and Long, Brian and Madigan, Zach and Malloy, Jessica and Malone, Jocelin and Maltzer, Zoe and Martin, Naomi and McCue, Rachel and McGinty, Ryan and Mei, Nicholas and Melchor, Jose and Meyerdierks, Emma and Mollenkopf, Tyler and Moonsman, Skyler and Nguyen, Thuc Nghi and Otto, Sven and Pham, Trangthanh and Rimorin, Christine and Ruiz, Augustin and Sanchez, Raymond and Sawyer, Lane and Shapovalova, Nadiya and Shepard, Noah and Slaughterbeck, Cliff and Sulc, Josef and Tieu, Michael and Torkelson, Amy and Tung, Herman and Valera Cuevas, Nasmil and Vance, Shane and Wadhwani, Katherine and Ward, Katelyn and Levi, Boaz and Farrell, Colin and Young, Rob and Staats, Brian and Wang, Ming-Qiang Michael and Thompson, Carol L. and Mufti, Shoaib and Pagan, Chelsea M. and Kruse, Lauren and Dee, Nick and Sunkin, Susan M. and Esposito, Luke and Hawrylycz, Michael J. and Waters, Jack and Ng, Lydia and Smith, Kimberly and Tasic, Bosiljka and Zhuang, Xiaowei and Zeng, Hongkui},
year = {2023},
month = Dec,
pages = {317–332}
}Source: alleninstitute.github.io ↗ · License: Allen Institute Terms of Use ↗ · Reprocessed to SpatialData by SpatialData-DB