Imaging Mass Cytometry
Human kidney
S-BIAD3694:discovery:Batch11:AIN-01-0150:kidney
bronze acute tubulointerstitial nephritis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'img_Batch11_001_image': DataTree[cyx] (35, 989, 765), (35, 494, 382), (35, 247, 191), (35, 123, 95), (35, 61, 47)
│ ├── 'img_Batch11_002_image': DataTree[cyx] (35, 4264, 678), (35, 2132, 339), (35, 1066, 169), (35, 533, 84), (35, 266, 42)
│ ├── 'img_Batch11_003_image': DataTree[cyx] (35, 1149, 882), (35, 574, 441), (35, 287, 220), (35, 143, 110), (35, 71, 55)
│ ├── 'img_Batch11_004_image': DataTree[cyx] (35, 1165, 1008), (35, 582, 504), (35, 291, 252), (35, 145, 126), (35, 72, 63)
│ └── 'img_Batch11_005_image': DataTree[cyx] (35, 1027, 828), (35, 513, 414), (35, 256, 207), (35, 128, 103), (35, 64, 51)
├── Labels
│ ├── 'img_Batch11_001_cells_labels': DataTree[yx] (989, 765), (494, 382), (247, 191), (123, 95), (61, 47)
│ ├── 'img_Batch11_002_cells_labels': DataTree[yx] (4264, 678), (2132, 339), (1066, 169), (533, 84), (266, 42)
│ ├── 'img_Batch11_003_cells_labels': DataTree[yx] (1149, 882), (574, 441), (287, 220), (143, 110), (71, 55)
│ ├── 'img_Batch11_004_cells_labels': DataTree[yx] (1165, 1008), (582, 504), (291, 252), (145, 126), (72, 63)
│ └── 'img_Batch11_005_cells_labels': DataTree[yx] (1027, 828), (513, 414), (256, 207), (128, 103), (64, 51)
├── Shapes
│ ├── 'img_Batch11_001_cell_boundaries': GeoDataFrame shape: (3006, 2) (2D shapes)
│ ├── 'img_Batch11_002_cell_boundaries': GeoDataFrame shape: (15389, 2) (2D shapes)
│ ├── 'img_Batch11_003_cell_boundaries': GeoDataFrame shape: (5483, 2) (2D shapes)
│ ├── 'img_Batch11_004_cell_boundaries': GeoDataFrame shape: (4238, 2) (2D shapes)
│ └── 'img_Batch11_005_cell_boundaries': GeoDataFrame shape: (4263, 2) (2D shapes)
└── Tables
└── 'table': AnnData (32379, 35)
with coordinate systems:
▸ 'img_Batch11_001', with elements:
img_Batch11_001_image (Images), img_Batch11_001_cells_labels (Labels), img_Batch11_001_cell_boundaries (Shapes)
▸ 'img_Batch11_002', with elements:
img_Batch11_002_image (Images), img_Batch11_002_cells_labels (Labels), img_Batch11_002_cell_boundaries (Shapes)
▸ 'img_Batch11_003', with elements:
img_Batch11_003_image (Images), img_Batch11_003_cells_labels (Labels), img_Batch11_003_cell_boundaries (Shapes)
▸ 'img_Batch11_004', with elements:
img_Batch11_004_image (Images), img_Batch11_004_cells_labels (Labels), img_Batch11_004_cell_boundaries (Shapes)
▸ 'img_Batch11_005', with elements:
img_Batch11_005_image (Images), img_Batch11_005_cells_labels (Labels), img_Batch11_005_cell_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("cXzUnDfdSns9QmwX0000")
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("cXzUnDfdSns9QmwX") # 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 cXzUnDfdSns9QmwX0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cXzUnDfdSns9QmwX
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cXzUnDfdSns9QmwXLicense: CC0 1.0
Metadata
- Technology
- Imaging Mass Cytometry
- Organism
- human
- Tissue
- kidney
- Condition
- acute tubulointerstitial nephritis
- Modality
- protein
- Observations (cells)
- 32,379
- Tier
- bronze
- Chemistry
- IMC
- Staining
- Antibodies
- Size
- 193 MB
- Sample ID
- S-BIAD3694:discovery:Batch11:AIN-01-0150: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