spatial transcriptomics

Human breast

SPA151

bronze H&E invasive ductal breast carcinoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'SPA151_full_image': DataTree[cyx] (3, 7424, 6975), (3, 3712, 3487), (3, 1856, 1743), (3, 928, 871)
├── Shapes
│     └── 'SPA151_spots': GeoDataFrame shape: (343, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (343, 15324)
with coordinate systems:
    ▸ 'global', with elements:
        SPA151_full_image (Images), SPA151_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("Dj0VCFzv4bziygII0001")
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("Dj0VCFzv4bziygII")   # 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 Dj0VCFzv4bziygII0001 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Dj0VCFzv4bziygII

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Dj0VCFzv4bziygII

Install (Python 3.12+) Docs →

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

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Part of collection

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions→

36 datasets · replicates

Metadata

Technology: spatial transcriptomics
Organism: human
Tissue: breast
Condition: invasive ductal breast carcinoma
Modality: RNA
Observations (spots): 343
Tier: bronze
Chemistry: ST 1k
Resolution: 6,975 × 7,424 px
mpp: 0.921 µm/px
Size: 89.6 MB
Sample ID: SPA151
License: CC BY-NC-SA 4.0 NonCommercial
Published: Sep 16, 2021

Cite this dataset

doi.org/10.1038/s41467-021-26271-2 ↗

BibTeX

@article{Andersson_2021,
  title = {Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions},
  volume = {12},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-021-26271-2},
  DOI = {10.1038/s41467-021-26271-2},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Andersson, Alma and Larsson, Ludvig and Stenbeck, Linnea and Salmén, Fredrik and Ehinger, Anna and Wu, Sunny Z. and Al-Eryani, Ghamdan and Roden, Daniel and Swarbrick, Alex and Borg, Åke and Frisén, Jonas and Engblom, Camilla and Lundeberg, Joakim},
  year = {2021},
  month = Oct
}

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