CosMx
Human pancreas
cosmx-wtx
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Points
│ └── 'points': DataFrame with shape: (328971185, 12) (2D points)
├── Shapes
│ ├── 'cells_polygons': GeoDataFrame shape: (48951, 9) (2D shapes)
│ ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (48944, 2) (2D shapes)
│ └── 'fov_boxes': GeoDataFrame shape: (18, 2) (2D shapes)
└── Tables
└── 'table': AnnData (48944, 21731)
with coordinate systems:
▸ 'global', with elements:
points (Points), cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("wfVFQEPZXA65gc8S0000")
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("wfVFQEPZXA65gc8S") # 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 wfVFQEPZXA65gc8S0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/wfVFQEPZXA65gc8S
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid wfVFQEPZXA65gc8SLicense: Bruker terms of use (pending review) (noncommercial)
Metadata
- Technology
- CosMx
- Organism
- human
- Tissue
- pancreas
- Modality
- RNA
- Observations (cells)
- 48,944
- Transcripts
- 65,794,237
- Tier
- silver
- Chemistry
- CosMx WTx
- Size
- 953 MB
- Sample ID
- cosmx-wtx
- License
- Bruker terms of use (pending review) NonCommercial
- Published
- Jan 7, 2024
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