Imaging Mass Cytometry
Human liver
S-BIAD2091:NASH_HCC_TMA-2_007
bronze No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'img_NASH_HCC_TMA-2_007_image': DataTree[cyx] (41, 1000, 1000), (41, 500, 500), (41, 250, 250), (41, 125, 125), (41, 62, 62)
├── Labels
│ └── 'img_NASH_HCC_TMA-2_007_cells_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (3959, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (3959, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3959, 41)
with coordinate systems:
▸ 'global', with elements:
img_NASH_HCC_TMA-2_007_image (Images), img_NASH_HCC_TMA-2_007_cells_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("gSjuItHpDBSJamvc0000")
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("gSjuItHpDBSJamvc") # 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 gSjuItHpDBSJamvc0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/gSjuItHpDBSJamvc
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid gSjuItHpDBSJamvcLicense: CC0 1.0
Metadata
- Technology
- Imaging Mass Cytometry
- Organism
- human
- Tissue
- liver
- Modality
- protein
- Observations (cells)
- 3,959
- Tier
- bronze
- Chemistry
- IMC
- Staining
- Antibodies
- Size
- 36.9 MB
- Sample ID
- S-BIAD2091:NASH_HCC_TMA-2_007
- License
- CC0 1.0
- Published
- Jul 9, 2025
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