spatial transcriptomics

Mouse brain

NCBI398

silver Interactive viewer H&E ✓ Verified publication

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print(sdata)

SpatialData object
├── Images
│     └── 'NCBI398_full_image': DataTree[cyx] (3, 9900, 9270), (3, 4950, 4635), (3, 2475, 2317), (3, 1237, 1158)
├── Shapes
│     └── 'NCBI398_spots': GeoDataFrame shape: (488, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (488, 21570)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI398_full_image (Images), NCBI398_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("06KiDxB6JkUcoKLR0001")
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("06KiDxB6JkUcoKLR")   # 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 06KiDxB6JkUcoKLR0001 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/06KiDxB6JkUcoKLR

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 06KiDxB6JkUcoKLR

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): 488
Tier: silver
Chemistry: ST 1k
Resolution: 9,270 × 9,900 px
mpp: 0.690 µm/px
Size: 130 MB
Sample ID: NCBI398
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