Visium
Human mammary gland
GSM6177603
bronze Interactive viewer H&E breast carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM6177603_NYU_BRCA2_Vis_processed_hires_image': DataArray[cyx] (3, 1964, 2000)
│ └── 'GSM6177603_NYU_BRCA2_Vis_processed_lowres_image': DataArray[cyx] (3, 589, 600)
├── Shapes
│ └── 'GSM6177603_NYU_BRCA2_Vis_processed': GeoDataFrame shape: (2346, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2346, 33538)
with coordinate systems:
▸ 'GSM6177603_NYU_BRCA2_Vis_processed', with elements:
GSM6177603_NYU_BRCA2_Vis_processed_hires_image (Images), GSM6177603_NYU_BRCA2_Vis_processed_lowres_image (Images), GSM6177603_NYU_BRCA2_Vis_processed (Shapes)
▸ 'GSM6177603_NYU_BRCA2_Vis_processed_downscaled_hires', with elements:
GSM6177603_NYU_BRCA2_Vis_processed_hires_image (Images), GSM6177603_NYU_BRCA2_Vis_processed (Shapes)
▸ 'GSM6177603_NYU_BRCA2_Vis_processed_downscaled_lowres', with elements:
GSM6177603_NYU_BRCA2_Vis_processed_lowres_image (Images), GSM6177603_NYU_BRCA2_Vis_processed (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("clyHb1Wl33HF1pLB0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("clyHb1Wl33HF1pLB") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download clyHb1Wl33HF1pLB0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/clyHb1Wl33HF1pLB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid clyHb1Wl33HF1pLBLicense: NCBI GEO policy
Part of collection
Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment→ 12 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- mammary gland
- Condition
- breast carcinoma
- Modality
- RNA
- Observations (spots)
- 2,346
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,964 px
- mpp
- 3.435 µm/px
- Size
- 34.3 MB
- Sample ID
- GSM6177603
- License
- NCBI GEO policy
- Published
- Aug 5, 2022
Cite this dataset
doi.org/10.1038/s41588-022-01141-9 ↗ BibTeX
@article{Barkley_2022,
title = {Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment},
volume = {54},
ISSN = {1546-1718},
url = {http://dx.doi.org/10.1038/s41588-022-01141-9},
DOI = {10.1038/s41588-022-01141-9},
number = {8},
journal = {Nature Genetics},
publisher = {Springer Science and Business Media LLC},
author = {Barkley, Dalia and Moncada, Reuben and Pour, Maayan and Liberman, Deborah A. and Dryg, Ian and Werba, Gregor and Wang, Wei and Baron, Maayan and Rao, Anjali and Xia, Bo and França, Gustavo S. and Weil, Alejandro and Delair, Deborah F. and Hajdu, Cristina and Lund, Amanda W. and Osman, Iman and Yanai, Itai},
year = {2022},
month = Aug,
pages = {1192–1201}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB