Visium
Human lymph node
NCBI683
silver Interactive viewer H&E invasive ductal breast carcinoma ✓ Verified publication
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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Q5vpfHy7jdA5y3Ct") # 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/Q5vpfHy7jdA5y3Ct
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Q5vpfHy7jdA5y3Ct Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Q5vpfHy7jdA5y3Ct0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 4,992
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 29,616 × 30,094 px
- mpp
- 0.273 µm/px
- Size
- 2.2 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