MERFISH

Mouse brain

Zhuang-ABCA-2.045

silver Interactive viewer ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Shapes
│     └── 'cell_circles': GeoDataFrame shape: (29628, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (29628, 1122)
with coordinate systems:
    ▸ 'global', with elements:
        cell_circles (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("7R4658pDKvHqyWEy0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("7R4658pDKvHqyWEy")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download 7R4658pDKvHqyWEy0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7R4658pDKvHqyWEy

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7R4658pDKvHqyWEy

Install (Python 3.12+) Docs →

License: Allen Institute Terms of Use (noncommercial)

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

abc-zhuang-abca-2→

66 datasets · publication

Metadata

Technology: MERFISH
Organism: mouse
Tissue: brain
Modality: RNA
Observations (cells): 29,628
Tier: silver
Size: 17.6 MB
Sample ID: Zhuang-ABCA-2.045
License: Allen Institute Terms of Use NonCommercial
Published: Dec 13, 2023

Cite this dataset

doi.org/10.1038/s41586-023-06808-9 ↗

BibTeX

@article{Zhang_2023,
  title = {Molecularly defined and spatially resolved cell atlas of the whole mouse brain},
  volume = {624},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-023-06808-9},
  DOI = {10.1038/s41586-023-06808-9},
  number = {7991},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Zhang, Meng and Pan, Xingjie and Jung, Won and Halpern, Aaron R. and Eichhorn, Stephen W. and Lei, Zhiyun and Cohen, Limor and Smith, Kimberly A. and Tasic, Bosiljka and Yao, Zizhen and Zeng, Hongkui and Zhuang, Xiaowei},
  year = {2023},
  month = Dec,
  pages = {343–354}
}

Source: alleninstitute.github.io ↗ · License: Allen Institute Terms of Use ↗ · Reprocessed to SpatialData by SpatialData-DB