spatial transcriptomics

Mouse brain

SPA12

silver H&E ✓ Verified publication

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print(sdata)

SpatialData object
├── Images
│     └── 'SPA12_full_image': DataTree[cyx] (3, 9921, 9295), (3, 4960, 4647), (3, 2480, 2323), (3, 1240, 1161)
├── Shapes
│     └── 'SPA12_spots': GeoDataFrame shape: (264, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (264, 15500)
with coordinate systems:
    ▸ 'global', with elements:
        SPA12_full_image (Images), SPA12_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("qcSJRzjK2ZUVpxuu0000")
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("qcSJRzjK2ZUVpxuu")   # 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 qcSJRzjK2ZUVpxuu0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qcSJRzjK2ZUVpxuu

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qcSJRzjK2ZUVpxuu

Install (Python 3.12+) Docs →

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

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Part of collection

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Metadata

Technology: spatial transcriptomics
Organism: mouse
Tissue: brain
Modality: RNA
Observations (spots): 264
Tier: silver
Chemistry: ST 1k
Resolution: 9,295 × 9,921 px
mpp: 0.685 µm/px
Size: 150 MB
Sample ID: SPA12
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jul 1, 2016

Cite this dataset

doi.org/10.1126/science.aaf2403 ↗

BibTeX

@article{St_hl_2016,
  title = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics},
  volume = {353},
  ISSN = {1095-9203},
  url = {http://dx.doi.org/10.1126/science.aaf2403},
  DOI = {10.1126/science.aaf2403},
  number = {6294},
  journal = {Science},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Ståhl, Patrik L. and Salmén, Fredrik and Vickovic, Sanja and Lundmark, Anna and Navarro, José Fernández and Magnusson, Jens and Giacomello, Stefania and Asp, Michaela and Westholm, Jakub O. and Huss, Mikael and Mollbrink, Annelie and Linnarsson, Sten and Codeluppi, Simone and Borg, Åke and Pontén, Fredrik and Costea, Paul Igor and Sahlén, Pelin and Mulder, Jan and Bergmann, Olaf and Lundeberg, Joakim and Frisén, Jonas},
  year = {2016},
  month = July,
  pages = {78–82}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB