CosMx
Human tonsil
protein_tonsil_25
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Shapes
│ ├── 'cells_polygons': GeoDataFrame shape: (1464516, 9) (2D shapes)
│ ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (1464516, 2) (2D shapes)
│ └── 'fov_boxes': GeoDataFrame shape: (383, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1464516, 69)
with coordinate systems:
▸ 'global', with elements:
cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("571yTEm4hqlkXRPf0000")
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("571yTEm4hqlkXRPf") # 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 571yTEm4hqlkXRPf0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/571yTEm4hqlkXRPf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 571yTEm4hqlkXRPfLicense: Bruker terms of use (pending review) (noncommercial)
Metadata
- Technology
- CosMx
- Organism
- human
- Tissue
- tonsil
- Modality
- protein
- Observations (cells)
- 1,464,516
- Tier
- silver
- Chemistry
- CosMx Protein 64-plex
- Size
- 1.3 GB
- Sample ID
- protein_tonsil_25
- License
- Bruker terms of use (pending review) NonCommercial
- Published
- Mar 28, 2025
Cite this dataset
No linked publication found — please cite the data source: brukerspatialbiology.com ↗.
Source: brukerspatialbiology.com ↗ · License: Bruker terms of use (pending review) ↗ · Reprocessed to SpatialData by SpatialData-DB