Imaging Mass Cytometry
Human kidney
S-BIAD3694:discovery:Batch8:AIN-01-0120:kidney
bronze acute tubulointerstitial nephritis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'img_Batch8_001_image': DataTree[cyx] (35, 2021, 741), (35, 1010, 370), (35, 505, 185), (35, 252, 92), (35, 126, 46)
│ ├── 'img_Batch8_002_image': DataTree[cyx] (35, 4935, 895), (35, 2467, 447), (35, 1233, 223), (35, 616, 111), (35, 308, 55)
│ ├── 'img_Batch8_003_image': DataTree[cyx] (35, 2835, 933), (35, 1417, 466), (35, 708, 233), (35, 354, 116), (35, 177, 58)
│ └── 'img_Batch8_004_image': DataTree[cyx] (35, 1441, 1071), (35, 720, 535), (35, 360, 267), (35, 180, 133), (35, 90, 66)
├── Labels
│ ├── 'img_Batch8_001_cells_labels': DataTree[yx] (2021, 741), (1010, 370), (505, 185), (252, 92), (126, 46)
│ ├── 'img_Batch8_002_cells_labels': DataTree[yx] (4935, 895), (2467, 447), (1233, 223), (616, 111), (308, 55)
│ ├── 'img_Batch8_003_cells_labels': DataTree[yx] (2835, 933), (1417, 466), (708, 233), (354, 116), (177, 58)
│ └── 'img_Batch8_004_cells_labels': DataTree[yx] (1441, 1071), (720, 535), (360, 267), (180, 133), (90, 66)
├── Shapes
│ ├── 'img_Batch8_001_cell_boundaries': GeoDataFrame shape: (8542, 2) (2D shapes)
│ ├── 'img_Batch8_002_cell_boundaries': GeoDataFrame shape: (21135, 2) (2D shapes)
│ ├── 'img_Batch8_003_cell_boundaries': GeoDataFrame shape: (15774, 2) (2D shapes)
│ └── 'img_Batch8_004_cell_boundaries': GeoDataFrame shape: (5008, 2) (2D shapes)
└── Tables
└── 'table': AnnData (50459, 35)
with coordinate systems:
▸ 'img_Batch8_001', with elements:
img_Batch8_001_image (Images), img_Batch8_001_cells_labels (Labels), img_Batch8_001_cell_boundaries (Shapes)
▸ 'img_Batch8_002', with elements:
img_Batch8_002_image (Images), img_Batch8_002_cells_labels (Labels), img_Batch8_002_cell_boundaries (Shapes)
▸ 'img_Batch8_003', with elements:
img_Batch8_003_image (Images), img_Batch8_003_cells_labels (Labels), img_Batch8_003_cell_boundaries (Shapes)
▸ 'img_Batch8_004', with elements:
img_Batch8_004_image (Images), img_Batch8_004_cells_labels (Labels), img_Batch8_004_cell_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("99ho3BLR2A1cskFg0000")
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("99ho3BLR2A1cskFg") # 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 99ho3BLR2A1cskFg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/99ho3BLR2A1cskFg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 99ho3BLR2A1cskFgLicense: CC0 1.0
Metadata
- Technology
- Imaging Mass Cytometry
- Organism
- human
- Tissue
- kidney
- Condition
- acute tubulointerstitial nephritis
- Modality
- protein
- Observations (cells)
- 50,459
- Tier
- bronze
- Chemistry
- IMC
- Staining
- Antibodies
- Size
- 364 MB
- Sample ID
- S-BIAD3694:discovery:Batch8:AIN-01-0120: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