Vizgen MERSCOPE

Human middle temporal gyrus

H21.33.006.Cx28.MTG.02.007.1.01.09.04

silver Interactive viewer Alzheimer disease ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Shapes
│     └── 'cell_circles': GeoDataFrame shape: (14762, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (14762, 140)
with coordinate systems:
    ▸ 'global', with elements:
        cell_circles (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("3KrCpO4UahZNb1Om0000")
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("3KrCpO4UahZNb1Om")   # 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 3KrCpO4UahZNb1Om0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3KrCpO4UahZNb1Om

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3KrCpO4UahZNb1Om

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

seaad-mtg-merfish→

64 datasets · replicates

Metadata

Technology: Vizgen MERSCOPE
Organism: human
Tissue: middle temporal gyrus
Condition: Alzheimer disease
Modality: RNA
Observations (cells): 14,762
Tier: silver
Size: 4.9 MB
Sample ID: H21.33.006.Cx28.MTG.02.007.1.01.09.04
License: Allen Institute Terms of Use NonCommercial
Published: Dec 11, 2024

Cite this dataset

doi.org/10.1038/s41593-024-01774-5 ↗

BibTeX

@article{seaad:MTG-MERFISH,
  author = {Gabitto, Mariano I. and Travaglini, Kyle J. and others},
  title = {Integrated multimodal cell atlas of Alzheimer's disease},
  journal = {Nature Neuroscience},
  year = {2024},
  volume = {27},
  pages = {2366--2383},
  doi = {10.1038/s41593-024-01774-5},
  note = {Dataset: Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD), middle temporal gyrus MERFISH (SEAAD_MTG_MERFISH.2024-12-11), https://sea-ad-spatial-transcriptomics.s3.us-west-2.amazonaws.com/middle-temporal-gyrus/. Allen Institute Terms of Use, https://alleninstitute.org/terms-of-use/}
}

Source: portal.brain-map.org ↗ · License: Allen Institute Terms of Use ↗ · Reprocessed to SpatialData by SpatialData-DB