Visium
Mouse brain
MEND124
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'MEND124_full_image': DataTree[cyx] (3, 47104, 44544), (3, 23552, 22272), (3, 11776, 11136), (3, 5888, 5568)
├── Shapes
│ └── 'MEND124_spots': GeoDataFrame shape: (1448, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1448, 32285)
with coordinate systems:
▸ 'global', with elements:
MEND124_full_image (Images), MEND124_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Pcsgu4flSQJOKFxL") # 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/Pcsgu4flSQJOKFxL
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Pcsgu4flSQJOKFxL Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Pcsgu4flSQJOKFxL0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 1,448
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 44,544 × 47,104 px
- mpp
- 0.172 µm/px
- Size
- 884 MB
- Sample ID
- MEND124
- 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