Visium
Mouse brain
MEND131
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MEND131_full_image': DataTree[cyx] (3, 15821, 15821), (3, 7910, 7910), (3, 3955, 3955), (3, 1977, 1977)
├── Shapes
│ └── 'MEND131_spots': GeoDataFrame shape: (1301, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1301, 31053)
with coordinate systems:
▸ 'global', with elements:
MEND131_full_image (Images), MEND131_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("bhhF3jCxyGVoJWsr0000")
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("bhhF3jCxyGVoJWsr") # 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 bhhF3jCxyGVoJWsr0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/bhhF3jCxyGVoJWsr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid bhhF3jCxyGVoJWsrLicense: CC BY-NC-SA 4.0 (noncommercial)
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 1,301
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 15,821 × 15,821 px
- mpp
- 0.574 µm/px
- Size
- 528 MB
- Sample ID
- MEND131
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Aug 15, 2023
Cite this dataset
doi.org/10.1101/2022.10.25.513696 ↗ BibTeX
@article{Fan_2022,
title = {Expansion Spatial Transcriptomics},
url = {http://dx.doi.org/10.1101/2022.10.25.513696},
DOI = {10.1101/2022.10.25.513696},
publisher = {openRxiv},
author = {Fan, Yuhang and Andrusivová, Žaneta and Wu, Yunming and Chai, Chew and Larsson, Ludvig and He, Mengxiao and Luo, Liqun and Lundeberg, Joakim and Wang, Bo},
year = {2022},
month = Oct
}Source: biorxiv.org ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB