MALDI mass spectrometry imaging
Mouse liver
2022-04-11_10h26m29s
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'optical_image': DataTree[cyx] (3, 1991, 1991), (3, 995, 995), (3, 497, 497), (3, 248, 248)
├── Shapes
│ └── 'maldi_spots': GeoDataFrame shape: (10000, 2) (2D shapes)
└── Tables
└── 'table': AnnData (10000, 37)
with coordinate systems:
▸ 'global', with elements:
optical_image (Images), maldi_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yCD7OmEeESs1d3Ei0000")
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("yCD7OmEeESs1d3Ei") # 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 yCD7OmEeESs1d3Ei0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yCD7OmEeESs1d3Ei
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yCD7OmEeESs1d3EiLicense: CC BY 4.0
Metadata
- Technology
- MALDI mass spectrometry imaging
- Organism
- mouse
- Tissue
- liver
- Modality
- Metabolomics
- Observations
- 10,000
- Tier
- bronze
- Magnification
- 40x
- Resolution
- 1,991 × 1,991 px
- mpp
- 10.000 µm/px
- Size
- 14.8 MB
- Sample ID
- 2022-04-11_10h26m29s
- License
- CC BY 4.0
- Published
- Jul 24, 2024
Cite this dataset
doi.org/10.1038/s42255-024-01118-4 ↗ BibTeX
@article{metaspace:2022-04-11_10h26m29s,
doi = {10.1038/s42255-024-01118-4},
title = {2022-04-11_10h26m29s},
year = {2024}
}Source: metaspace2020.org ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB