spatial transcriptomics

Mouse brain

NCBI339

silver Interactive viewer H&E ✓ Verified publication

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print(sdata)

SpatialData object
├── Images
│     └── 'NCBI339_full_image': DataTree[cyx] (3, 9853, 9319), (3, 4926, 4659), (3, 2463, 2329), (3, 1231, 1164)
├── Shapes
│     └── 'NCBI339_spots': GeoDataFrame shape: (245, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (245, 21473)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI339_full_image (Images), NCBI339_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("vKjigC5yMxPTUKEQ0000")
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("vKjigC5yMxPTUKEQ")   # 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 vKjigC5yMxPTUKEQ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/vKjigC5yMxPTUKEQ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vKjigC5yMxPTUKEQ

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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Part of collection

Molecular Atlas of the Adult Mouse Brain→

75 datasets · publication

Metadata

Technology: spatial transcriptomics
Organism: mouse
Tissue: brain
Modality: RNA
Observations (spots): 245
Tier: silver
Chemistry: ST 1k
Resolution: 9,319 × 9,853 px
mpp: 0.693 µm/px
Size: 199 MB
Sample ID: NCBI339
License: CC BY-NC-SA 4.0 NonCommercial
Published: May 3, 2020

Cite this dataset

doi.org/10.1126/sciadv.abb3446 ↗

BibTeX

@article{Ortiz_2020,
  title = {Molecular atlas of the adult mouse brain},
  volume = {6},
  ISSN = {2375-2548},
  url = {http://dx.doi.org/10.1126/sciadv.abb3446},
  DOI = {10.1126/sciadv.abb3446},
  number = {26},
  journal = {Science Advances},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Ortiz, Cantin and Navarro, Jose Fernandez and Jurek, Aleksandra and Märtin, Antje and Lundeberg, Joakim and Meletis, Konstantinos},
  year = {2020},
  month = June
}

Source: science.org ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB