Visium
Human kidney
NCBI539
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI539_full_image': DataTree[cyx] (3, 47104, 48640), (3, 23552, 24320), (3, 11776, 12160), (3, 5888, 6080)
├── Shapes
│ └── 'NCBI539_spots': GeoDataFrame shape: (475, 2) (2D shapes)
└── Tables
└── 'table': AnnData (475, 33538)
with coordinate systems:
▸ 'global', with elements:
NCBI539_full_image (Images), NCBI539_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("iWW4QFCrsSD1AZ5w0000")
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("iWW4QFCrsSD1AZ5w") # 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 iWW4QFCrsSD1AZ5w0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/iWW4QFCrsSD1AZ5w
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iWW4QFCrsSD1AZ5wLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues→ 15 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- kidney
- Modality
- RNA
- Observations (spots)
- 475
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 48,640 × 47,104 px
- mpp
- 0.174 µm/px
- Size
- 2.3 GB
- Sample ID
- NCBI539
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Oct 15, 2021
Cite this dataset
doi.org/10.1016/j.xgen.2021.100065 ↗ BibTeX
@article{Gracia_Villacampa_2021,
title = {Genome-wide spatial expression profiling in formalin-fixed tissues},
volume = {1},
ISSN = {2666-979X},
url = {http://dx.doi.org/10.1016/j.xgen.2021.100065},
DOI = {10.1016/j.xgen.2021.100065},
number = {3},
journal = {Cell Genomics},
publisher = {Elsevier BV},
author = {Gracia Villacampa, Eva and Larsson, Ludvig and Mirzazadeh, Reza and Kvastad, Linda and Andersson, Alma and Mollbrink, Annelie and Kokaraki, Georgia and Monteil, Vanessa and Schultz, Niklas and Appelberg, Karin Sofia and Montserrat, Nuria and Zhang, Haibo and Penninger, Josef M. and Miesbach, Wolfgang and Mirazimi, Ali and Carlson, Joseph and Lundeberg, Joakim},
year = {2021},
month = Dec,
pages = {100065}
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB