MALDI mass spectrometry imaging
Human kidney
2023-01-17_22h30m56s
bronze Interactive viewer H&E cancer ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'optical_image': DataTree[cyx] (3, 2053, 3094), (3, 1026, 1547), (3, 513, 773), (3, 256, 386)
├── Shapes
│ └── 'maldi_spots': GeoDataFrame shape: (403263, 2) (2D shapes)
└── Tables
└── 'table': AnnData (403263, 2)
with coordinate systems:
▸ 'global', with elements:
optical_image (Images), maldi_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("D4PmvrhoPZEkaQdt0000")
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("D4PmvrhoPZEkaQdt") # 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 D4PmvrhoPZEkaQdt0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/D4PmvrhoPZEkaQdt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid D4PmvrhoPZEkaQdtLicense: CC BY 4.0
Metadata
- Technology
- MALDI mass spectrometry imaging
- Organism
- human
- Tissue
- kidney
- Condition
- cancer
- Modality
- Metabolomics
- Observations
- 403,263
- Tier
- bronze
- Resolution
- 3,094 × 2,053 px
- mpp
- 40.000 µm/px
- Size
- 15.9 MB
- Sample ID
- 2023-01-17_22h30m56s
- License
- CC BY 4.0
- Published
- Jan 4, 2024
Cite this dataset
doi.org/10.1038/s41598-023-50957-w ↗ BibTeX
@article{metaspace:2023-01-17_22h30m56s,
doi = {10.1038/s41598-023-50957-w},
title = {2023-01-17_22h30m56s},
year = {2024}
}Source: metaspace2020.org ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB