Visium

Human lymph node

NCBI683

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

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI683_full_image': DataTree[cyx] (3, 30094, 29616), (3, 15047, 14808), (3, 7523, 7404), (3, 3761, 3702)
├── Shapes
│     └── 'NCBI683_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 33931)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI683_full_image (Images), NCBI683_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("Q5vpfHy7jdA5y3Ct0000")
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("Q5vpfHy7jdA5y3Ct")   # 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 Q5vpfHy7jdA5y3Ct0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Q5vpfHy7jdA5y3Ct

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Q5vpfHy7jdA5y3Ct

Install (Python 3.12+) Docs →

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

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Part of collection

Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients→

4 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: lymph node
Condition: invasive ductal breast carcinoma
Modality: RNA
Observations (spots): 4,992
Tier: silver
Chemistry: Visium v1
Magnification: 40x
Resolution: 29,616 × 30,094 px
mpp: 0.273 µm/px
Size: 2.4 GB
Sample ID: NCBI683
License: CC BY-NC-SA 4.0 NonCommercial
Published: Apr 30, 2022

Cite this dataset

doi.org/10.1038/s41467-022-34581-2 ↗

BibTeX

@article{Liu_2022,
  title = {Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients},
  volume = {13},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-022-34581-2},
  DOI = {10.1038/s41467-022-34581-2},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Liu, Tong and Liu, Cheng and Yan, Meisi and Zhang, Lei and Zhang, Jing and Xiao, Min and Li, Zhigao and Wei, Xiaofan and Zhang, Hongquan},
  year = {2022},
  month = Nov
}

Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB