spatial transcriptomics

Human breast

SPA129

silver Interactive viewer H&E invasive ductal breast carcinoma Provisional

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'SPA129_full_image': DataTree[cyx] (3, 9862, 9308), (3, 4931, 4654), (3, 2465, 2327), (3, 1232, 1163)
├── Shapes
│     └── 'SPA129_spots': GeoDataFrame shape: (572, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (572, 14928)
with coordinate systems:
    ▸ 'global', with elements:
        SPA129_full_image (Images), SPA129_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("zo2fTMRoAL96vc3J")   # 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

Load from the CLI

# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/zo2fTMRoAL96vc3J

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid zo2fTMRoAL96vc3J

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["zo2fTMRoAL96vc3J0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

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: 572
Tier: silver
Chemistry: ST 1k
Resolution: 9,308 × 9,862 px
mpp: 0.688 µm/px
Size: 206 MB
Sample ID: SPA129
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