spatial transcriptomics
Human breast
SPA152
silver Interactive viewer H&E invasive ductal breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'SPA152_full_image': DataTree[cyx] (3, 7437, 6935), (3, 3718, 3467), (3, 1859, 1733), (3, 929, 866)
├── Shapes
│ └── 'SPA152_spots': GeoDataFrame shape: (359, 2) (2D shapes)
└── Tables
└── 'table': AnnData (359, 15258)
with coordinate systems:
▸ 'global', with elements:
SPA152_full_image (Images), SPA152_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ND1IkQbCPNbcQqms") # 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/ND1IkQbCPNbcQqms
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ND1IkQbCPNbcQqms Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ND1IkQbCPNbcQqms0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart 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
- 359
- Tier
- silver
- Chemistry
- ST 1k
- Resolution
- 6,935 × 7,437 px
- mpp
- 0.921 µm/px
- Size
- 89 MB
- Sample ID
- SPA152
- 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