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Imaging Mass Cytometry

Human kidney

S-BIAD3694:discovery:Batch10:AIN-01-0123:kidney

bronze acute tubulointerstitial nephritis ✓ Verified publication
Imaging Mass Cytometry
print(sdata) 
SpatialData object
├── Images
│     ├── 'img_Batch10_006_image': DataTree[cyx] (35, 3387, 782), (35, 1693, 391), (35, 846, 195), (35, 423, 97), (35, 211, 48)
│     ├── 'img_Batch10_007_image': DataTree[cyx] (35, 2326, 847), (35, 1163, 423), (35, 581, 211), (35, 290, 105), (35, 145, 52)
│     ├── 'img_Batch10_008_image': DataTree[cyx] (35, 1287, 864), (35, 643, 432), (35, 321, 216), (35, 160, 108), (35, 80, 54)
│     ├── 'img_Batch10_009_image': DataTree[cyx] (35, 3750, 833), (35, 1875, 416), (35, 937, 208), (35, 468, 104), (35, 234, 52)
│     └── 'img_Batch10_010_image': DataTree[cyx] (35, 1340, 831), (35, 670, 415), (35, 335, 207), (35, 167, 103), (35, 83, 51)
├── Labels
│     ├── 'img_Batch10_006_cells_labels': DataTree[yx] (3387, 782), (1693, 391), (846, 195), (423, 97), (211, 48)
│     ├── 'img_Batch10_007_cells_labels': DataTree[yx] (2326, 847), (1163, 423), (581, 211), (290, 105), (145, 52)
│     ├── 'img_Batch10_008_cells_labels': DataTree[yx] (1287, 864), (643, 432), (321, 216), (160, 108), (80, 54)
│     ├── 'img_Batch10_009_cells_labels': DataTree[yx] (3750, 833), (1875, 416), (937, 208), (468, 104), (234, 52)
│     └── 'img_Batch10_010_cells_labels': DataTree[yx] (1340, 831), (670, 415), (335, 207), (167, 103), (83, 51)
├── Shapes
│     ├── 'img_Batch10_006_cell_boundaries': GeoDataFrame shape: (19217, 2) (2D shapes)
│     ├── 'img_Batch10_007_cell_boundaries': GeoDataFrame shape: (13497, 2) (2D shapes)
│     ├── 'img_Batch10_008_cell_boundaries': GeoDataFrame shape: (8210, 2) (2D shapes)
│     ├── 'img_Batch10_009_cell_boundaries': GeoDataFrame shape: (22938, 2) (2D shapes)
│     └── 'img_Batch10_010_cell_boundaries': GeoDataFrame shape: (7547, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (71409, 35)
with coordinate systems:
    ▸ 'img_Batch10_006', with elements:
        img_Batch10_006_image (Images), img_Batch10_006_cells_labels (Labels), img_Batch10_006_cell_boundaries (Shapes)
    ▸ 'img_Batch10_007', with elements:
        img_Batch10_007_image (Images), img_Batch10_007_cells_labels (Labels), img_Batch10_007_cell_boundaries (Shapes)
    ▸ 'img_Batch10_008', with elements:
        img_Batch10_008_image (Images), img_Batch10_008_cells_labels (Labels), img_Batch10_008_cell_boundaries (Shapes)
    ▸ 'img_Batch10_009', with elements:
        img_Batch10_009_image (Images), img_Batch10_009_cells_labels (Labels), img_Batch10_009_cell_boundaries (Shapes)
    ▸ 'img_Batch10_010', with elements:
        img_Batch10_010_image (Images), img_Batch10_010_cells_labels (Labels), img_Batch10_010_cell_boundaries (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("CjPuRkERIBM1Or3m0000")
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("CjPuRkERIBM1Or3m")   # 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 CjPuRkERIBM1Or3m0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CjPuRkERIBM1Or3m

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CjPuRkERIBM1Or3m
Install (Python 3.12+) Docs →

License: CC0 1.0

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Metadata

Technology
Imaging Mass Cytometry
Organism
human
Tissue
kidney
Condition
acute tubulointerstitial nephritis
Modality
protein
Observations (cells)
71,409
Tier
bronze
Chemistry
IMC
Staining
Antibodies
Size
456 MB
Sample ID
S-BIAD3694:discovery:Batch10:AIN-01-0123: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