spatial transcriptomics

Human breast

SPA150

silver Interactive viewer H&E invasive ductal breast carcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'SPA150_full_image': DataTree[cyx] (3, 7419, 6966), (3, 3709, 3483), (3, 1854, 1741), (3, 927, 870)
├── Shapes
│     └── 'SPA150_spots': GeoDataFrame shape: (332, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (332, 15388)
with coordinate systems:
    ▸ 'global', with elements:
        SPA150_full_image (Images), SPA150_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("3E0Wrfsge3mlI3YP0000")
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("3E0Wrfsge3mlI3YP")   # 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 3E0Wrfsge3mlI3YP0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3E0Wrfsge3mlI3YP

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3E0Wrfsge3mlI3YP

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): 332
Tier: silver
Chemistry: ST 1k
Resolution: 6,966 × 7,419 px
mpp: 0.946 µm/px
Size: 94.4 MB
Sample ID: SPA150
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