Imaging Mass Cytometry

Mouse lung

S-BIAD3184:slide1:mouse24

bronze Provisional

Imaging Mass Cytometry

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'img_m16263_slide1_004_image': DataTree[cyx] (76, 690, 660), (76, 345, 330), (76, 172, 165), (76, 86, 82), (76, 43, 41)
│     ├── 'img_m16263_slide1_005_image': DataTree[cyx] (76, 690, 660), (76, 345, 330), (76, 172, 165), (76, 86, 82), (76, 43, 41)
│     └── 'img_m16263_slide1_006_image': DataTree[cyx] (76, 690, 660), (76, 345, 330), (76, 172, 165), (76, 86, 82), (76, 43, 41)
├── Labels
│     ├── 'img_m16263_slide1_004_cells_labels': DataTree[yx] (690, 660), (345, 330), (172, 165), (86, 82), (43, 41)
│     ├── 'img_m16263_slide1_005_cells_labels': DataTree[yx] (690, 660), (345, 330), (172, 165), (86, 82), (43, 41)
│     └── 'img_m16263_slide1_006_cells_labels': DataTree[yx] (690, 660), (345, 330), (172, 165), (86, 82), (43, 41)
├── Shapes
│     ├── 'img_m16263_slide1_004_cell_boundaries': GeoDataFrame shape: (2029, 2) (2D shapes)
│     ├── 'img_m16263_slide1_005_cell_boundaries': GeoDataFrame shape: (1755, 2) (2D shapes)
│     └── 'img_m16263_slide1_006_cell_boundaries': GeoDataFrame shape: (1817, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (5601, 76)
with coordinate systems:
    ▸ 'img_m16263_slide1_004', with elements:
        img_m16263_slide1_004_image (Images), img_m16263_slide1_004_cells_labels (Labels), img_m16263_slide1_004_cell_boundaries (Shapes)
    ▸ 'img_m16263_slide1_005', with elements:
        img_m16263_slide1_005_image (Images), img_m16263_slide1_005_cells_labels (Labels), img_m16263_slide1_005_cell_boundaries (Shapes)
    ▸ 'img_m16263_slide1_006', with elements:
        img_m16263_slide1_006_image (Images), img_m16263_slide1_006_cells_labels (Labels), img_m16263_slide1_006_cell_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("ByqGm2xDMEUmfefE0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("ByqGm2xDMEUmfefE")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download ByqGm2xDMEUmfefE0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ByqGm2xDMEUmfefE

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ByqGm2xDMEUmfefE

Install (Python 3.12+) Docs →

License: CC BY 4.0

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Part of collection

bia-s-biad3184→

12 datasets · publication

Metadata

Technology: Imaging Mass Cytometry
Organism: mouse
Tissue: lung
Modality: protein
Observations (cells): 5,601
Tier: bronze
Chemistry: IMC
Staining: Antibodies
Size: 315 MB
Sample ID: S-BIAD3184:slide1:mouse24
License: CC BY 4.0
Published: Jun 23, 2026

Cite this dataset

doi.org/10.1101/2024.11.15.623782 ↗

BibTeX

@article{bia:S-BIAD3184,
  doi = {10.1101/2024.11.15.623782},
  title = {S-BIAD3184:slide3:mouse35},
  year = {2024}
}

Source: BioImage Archive ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB