Visium
Human uterus
NCBI691
silver Interactive viewer H&E endometriosis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI691_full_image': DataTree[cyx] (3, 15950, 15740), (3, 7975, 7870), (3, 3987, 3935), (3, 1993, 1967)
├── Shapes
│ └── 'NCBI691_spots': GeoDataFrame shape: (1388, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1388, 36601)
with coordinate systems:
▸ 'global', with elements:
NCBI691_full_image (Images), NCBI691_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("vJOkFGOWb7FOEdU2") # 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/vJOkFGOWb7FOEdU2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid vJOkFGOWb7FOEdU2 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["vJOkFGOWb7FOEdU20000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- uterus
- Condition
- endometriosis
- Modality
- RNA
- Observations
- 1,388
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 15,740 × 15,950 px
- mpp
- 0.504 µm/px
- Size
- 512 MB
- Sample ID
- NCBI691
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Oct 30, 2022
Cite this dataset
doi.org/10.1038/s41588-022-01254-1 ↗ BibTeX
@article{Fonseca_2023,
title = {Single-cell transcriptomic analysis of endometriosis},
volume = {55},
ISSN = {1546-1718},
url = {http://dx.doi.org/10.1038/s41588-022-01254-1},
DOI = {10.1038/s41588-022-01254-1},
number = {2},
journal = {Nature Genetics},
publisher = {Springer Science and Business Media LLC},
author = {Fonseca, Marcos A. S. and Haro, Marcela and Wright, Kelly N. and Lin, Xianzhi and Abbasi, Forough and Sun, Jennifer and Hernandez, Lourdes and Orr, Natasha L. and Hong, Jooyoon and Choi-Kuaea, Yunhee and Maluf, Horacio M. and Balzer, Bonnie L. and Fishburn, Aaron and Hickey, Ryan and Cass, Ilana and Goodridge, Helen S. and Truong, Mireille and Wang, Yemin and Pisarska, Margareta D. and Dinh, Huy Q. and EL-Naggar, Amal and Huntsman, David G. and Anglesio, Michael S. and Goodman, Marc T. and Medeiros, Fabiola and Siedhoff, Matthew and Lawrenson, Kate},
year = {2023},
month = Jan,
pages = {255–267}
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB