MIBI-TOF
Human breast
S-BIAD1288:TONIC_TMA4_R10C4
bronze triple-negative breast carcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'TONIC_TMA4_R10C4_image': DataTree[cyx] (53, 2048, 2048), (53, 1024, 1024), (53, 512, 512), (53, 256, 256), (53, 128, 128)
├── Labels
│ ├── 'TONIC_TMA4_R10C4_nuclear_labels': DataTree[yx] (2048, 2048), (1024, 1024), (512, 512), (256, 256), (128, 128)
│ └── 'TONIC_TMA4_R10C4_whole_cell_labels': DataTree[yx] (2048, 2048), (1024, 1024), (512, 512), (256, 256), (128, 128)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (2033, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (2033, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2033, 53)
with coordinate systems:
▸ 'global', with elements:
TONIC_TMA4_R10C4_image (Images), TONIC_TMA4_R10C4_nuclear_labels (Labels), TONIC_TMA4_R10C4_whole_cell_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("skIm8T14dXxGwrJB0000")
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("skIm8T14dXxGwrJB") # 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 skIm8T14dXxGwrJB0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/skIm8T14dXxGwrJB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid skIm8T14dXxGwrJBLicense: CC0 1.0
Metadata
- Technology
- MIBI-TOF
- Organism
- human
- Tissue
- breast
- Condition
- triple-negative breast carcinoma
- Modality
- protein
- Observations
- 2,033
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 475 MB
- Sample ID
- S-BIAD1288:TONIC_TMA4_R10C4
- License
- CC0 1.0
- Published
- Sep 28, 2024
Cite this dataset
No linked publication found — please cite the data source: BioImage Archive ↗.
Source: BioImage Archive ↗ · License: CC0 1.0 ↗ · Reprocessed to SpatialData by SpatialData-DB