MIBI-TOF
Human lymph node
S-BIAD1288:TONIC_TMA14_R10C1
bronze triple-negative breast carcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'TONIC_TMA14_R10C1_image': DataTree[cyx] (51, 2048, 2048), (51, 1024, 1024), (51, 512, 512), (51, 256, 256), (51, 128, 128)
├── Labels
│ ├── 'TONIC_TMA14_R10C1_nuclear_labels': DataTree[yx] (2048, 2048), (1024, 1024), (512, 512), (256, 256), (128, 128)
│ └── 'TONIC_TMA14_R10C1_whole_cell_labels': DataTree[yx] (2048, 2048), (1024, 1024), (512, 512), (256, 256), (128, 128)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (3905, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (3905, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3905, 51)
with coordinate systems:
▸ 'global', with elements:
TONIC_TMA14_R10C1_image (Images), TONIC_TMA14_R10C1_nuclear_labels (Labels), TONIC_TMA14_R10C1_whole_cell_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("P9OsaxK129Pw5Hum0000")
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("P9OsaxK129Pw5Hum") # 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 P9OsaxK129Pw5Hum0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/P9OsaxK129Pw5Hum
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid P9OsaxK129Pw5HumLicense: CC0 1.0
Metadata
- Technology
- MIBI-TOF
- Organism
- human
- Tissue
- lymph node
- Condition
- triple-negative breast carcinoma
- Modality
- protein
- Observations
- 3,905
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 538 MB
- Sample ID
- S-BIAD1288:TONIC_TMA14_R10C1
- 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