MALDI mass spectrometry imaging
Human kidney
2021-09-02_21h44m18s
bronze Interactive viewer H&E diabetic kidney disease No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'optical_image': DataTree[cyx] (3, 10380, 11104), (3, 5190, 5552), (3, 2595, 2776), (3, 1297, 1388)
├── Shapes
│ └── 'maldi_spots': GeoDataFrame shape: (27384, 2) (2D shapes)
└── Tables
└── 'table': AnnData (27384, 4)
with coordinate systems:
▸ 'global', with elements:
optical_image (Images), maldi_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Binj4kMy92Ahb1in0000")
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("Binj4kMy92Ahb1in") # 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 Binj4kMy92Ahb1in0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Binj4kMy92Ahb1in
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Binj4kMy92Ahb1inLicense: CC BY 4.0
Metadata
- Technology
- MALDI mass spectrometry imaging
- Organism
- human
- Tissue
- kidney
- Condition
- diabetic kidney disease
- Modality
- Metabolomics
- Observations
- 27,384
- Tier
- bronze
- Magnification
- 40x
- Resolution
- 11,104 × 10,380 px
- mpp
- 35.000 µm/px
- Size
- 185 MB
- Sample ID
- 2021-09-02_21h44m18s
- License
- CC BY 4.0
- Published
- Sep 2, 2021
Cite this dataset
No linked publication found — please cite the data source: metaspace2020.org ↗.
Source: metaspace2020.org ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB