Visium
Human prostate gland
MEND60
silver Interactive viewer H&E prostatic acinar adenocarcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MEND60_full_image': DataTree[cyx] (3, 47104, 48640), (3, 23552, 24320), (3, 11776, 12160), (3, 5888, 6080)
├── Shapes
│ └── 'MEND60_spots': GeoDataFrame shape: (3954, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3954, 17943)
with coordinate systems:
▸ 'global', with elements:
MEND60_full_image (Images), MEND60_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("X6oSMy5SPhfuSSvo") # 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/X6oSMy5SPhfuSSvo
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid X6oSMy5SPhfuSSvo Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["X6oSMy5SPhfuSSvo0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatially resolved transcriptomic profiling of degraded→ 35 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- prostatic acinar adenocarcinoma
- Modality
- RNA
- Observations
- 3,954
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 48,640 × 47,104 px
- mpp
- 0.173 µm/px
- Size
- 4.3 GB
- Sample ID
- MEND60
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 20, 2022
Cite this dataset
doi.org/10.1038/s41467-023-36071-5 ↗ BibTeX
@article{Mirzazadeh_2023,
title = {Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-36071-5},
DOI = {10.1038/s41467-023-36071-5},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Mirzazadeh, Reza and Andrusivova, Zaneta and Larsson, Ludvig and Newton, Phillip T. and Galicia, Leire Alonso and Abalo, Xesús M. and Avijgan, Mahtab and Kvastad, Linda and Denadai-Souza, Alexandre and Stakenborg, Nathalie and Firsova, Alexandra B. and Shamikh, Alia and Jurek, Aleksandra and Schultz, Niklas and Nistér, Monica and Samakovlis, Christos and Boeckxstaens, Guy and Lundeberg, Joakim},
year = {2023},
month = Jan
}Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB