PhenoCycler
Human pancreas
7742474:reg001
bronze Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'reg001_image': DataTree[cyx] (12, 18440, 25816), (12, 9220, 12908), (12, 4610, 6454), (12, 2305, 3227), (12, 1152, 1613)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (269257, 1) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (269257, 2) (2D shapes)
└── Tables
└── 'table': AnnData (269257, 12)
with coordinate systems:
▸ 'global', with elements:
reg001_image (Images), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("6qkrnCQLRUpXgNMx0000")
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("6qkrnCQLRUpXgNMx") # 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 6qkrnCQLRUpXgNMx0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/6qkrnCQLRUpXgNMx
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 6qkrnCQLRUpXgNMxLicense: CC BY 4.0
Metadata
- Technology
- PhenoCycler
- Organism
- human
- Tissue
- pancreas
- Modality
- protein
- Observations (cells)
- 269,257
- Tier
- bronze
- Chemistry
- CODEX Processor
- Staining
- IF
- Size
- 8.2 GB
- Sample ID
- 7742474:reg001
- License
- CC BY 4.0
- Published
- Mar 16, 2023
Cite this dataset
No linked publication found — please cite the data source: doi.org ↗.
Source: doi.org ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB