Imaging Mass Cytometry

Human kidney

S-BIAD3694:discovery:Batch12:AIN-01-0151:kidney

bronze acute tubulointerstitial nephritis ✓ Verified publication

Imaging Mass Cytometry

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'img_Batch12_021_image': DataTree[cyx] (35, 811, 714), (35, 405, 357), (35, 202, 178), (35, 101, 89), (35, 50, 44)
│     └── 'img_Batch12_022_image': DataTree[cyx] (35, 1310, 703), (35, 655, 351), (35, 327, 175), (35, 163, 87), (35, 81, 43)
├── Labels
│     ├── 'img_Batch12_021_cells_labels': DataTree[yx] (811, 714), (405, 357), (202, 178), (101, 89), (50, 44)
│     └── 'img_Batch12_022_cells_labels': DataTree[yx] (1310, 703), (655, 351), (327, 175), (163, 87), (81, 43)
├── Shapes
│     ├── 'img_Batch12_021_cell_boundaries': GeoDataFrame shape: (2856, 2) (2D shapes)
│     └── 'img_Batch12_022_cell_boundaries': GeoDataFrame shape: (4412, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (7268, 35)
with coordinate systems:
    ▸ 'img_Batch12_021', with elements:
        img_Batch12_021_image (Images), img_Batch12_021_cells_labels (Labels), img_Batch12_021_cell_boundaries (Shapes)
    ▸ 'img_Batch12_022', with elements:
        img_Batch12_022_image (Images), img_Batch12_022_cells_labels (Labels), img_Batch12_022_cell_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("2p1kqlooLQMfDRuJ0000")
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("2p1kqlooLQMfDRuJ")   # 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 2p1kqlooLQMfDRuJ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/2p1kqlooLQMfDRuJ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 2p1kqlooLQMfDRuJ

Install (Python 3.12+) Docs →

License: CC0 1.0

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Part of collection

bia-s-biad3694→

67 datasets · publication

Metadata

Technology: Imaging Mass Cytometry
Organism: human
Tissue: kidney
Condition: acute tubulointerstitial nephritis
Modality: protein
Observations (cells): 7,268
Tier: bronze
Chemistry: IMC
Staining: Antibodies
Size: 48.4 MB
Sample ID: S-BIAD3694:discovery:Batch12:AIN-01-0151:kidney
License: CC0 1.0
Published: Aug 18, 2026

Cite this dataset

doi.org/10.1038/s41467-026-77210-y ↗

BibTeX

@article{bia:S-BIAD3694,
  doi = {10.1038/s41467-026-77210-y},
  title = {S-BIAD3694:discovery:Batch2:L108:kidney}
}

Source: BioImage Archive ↗ · License: CC0 1.0 ↗ · Reprocessed to SpatialData by SpatialData-DB