Imaging Mass Cytometry
Human kidney
S-BIAD3694:discovery:Batch9:AIN-01-0135:kidney
bronze acute tubulointerstitial nephritis ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'img_Batch9_016_image': DataTree[cyx] (35, 1374, 506), (35, 687, 253), (35, 343, 126), (35, 171, 63), (35, 85, 31)
│ ├── 'img_Batch9_017_image': DataTree[cyx] (35, 1573, 777), (35, 786, 388), (35, 393, 194), (35, 196, 97), (35, 98, 48)
│ ├── 'img_Batch9_018_image': DataTree[cyx] (35, 812, 827), (35, 406, 413), (35, 203, 206), (35, 101, 103), (35, 50, 51)
│ ├── 'img_Batch9_019_image': DataTree[cyx] (35, 803, 767), (35, 401, 383), (35, 200, 191), (35, 100, 95), (35, 50, 47)
│ └── 'img_Batch9_020_image': DataTree[cyx] (35, 860, 1060), (35, 430, 530), (35, 215, 265), (35, 107, 132), (35, 53, 66)
├── Labels
│ ├── 'img_Batch9_016_cells_labels': DataTree[yx] (1374, 506), (687, 253), (343, 126), (171, 63), (85, 31)
│ ├── 'img_Batch9_017_cells_labels': DataTree[yx] (1573, 777), (786, 388), (393, 194), (196, 97), (98, 48)
│ ├── 'img_Batch9_018_cells_labels': DataTree[yx] (812, 827), (406, 413), (203, 206), (101, 103), (50, 51)
│ ├── 'img_Batch9_019_cells_labels': DataTree[yx] (803, 767), (401, 383), (200, 191), (100, 95), (50, 47)
│ └── 'img_Batch9_020_cells_labels': DataTree[yx] (860, 1060), (430, 530), (215, 265), (107, 132), (53, 66)
├── Shapes
│ ├── 'img_Batch9_016_cell_boundaries': GeoDataFrame shape: (4934, 2) (2D shapes)
│ ├── 'img_Batch9_017_cell_boundaries': GeoDataFrame shape: (7868, 2) (2D shapes)
│ ├── 'img_Batch9_018_cell_boundaries': GeoDataFrame shape: (4248, 2) (2D shapes)
│ ├── 'img_Batch9_019_cell_boundaries': GeoDataFrame shape: (3121, 2) (2D shapes)
│ └── 'img_Batch9_020_cell_boundaries': GeoDataFrame shape: (3814, 2) (2D shapes)
└── Tables
└── 'table': AnnData (23985, 35)
with coordinate systems:
▸ 'img_Batch9_016', with elements:
img_Batch9_016_image (Images), img_Batch9_016_cells_labels (Labels), img_Batch9_016_cell_boundaries (Shapes)
▸ 'img_Batch9_017', with elements:
img_Batch9_017_image (Images), img_Batch9_017_cells_labels (Labels), img_Batch9_017_cell_boundaries (Shapes)
▸ 'img_Batch9_018', with elements:
img_Batch9_018_image (Images), img_Batch9_018_cells_labels (Labels), img_Batch9_018_cell_boundaries (Shapes)
▸ 'img_Batch9_019', with elements:
img_Batch9_019_image (Images), img_Batch9_019_cells_labels (Labels), img_Batch9_019_cell_boundaries (Shapes)
▸ 'img_Batch9_020', with elements:
img_Batch9_020_image (Images), img_Batch9_020_cells_labels (Labels), img_Batch9_020_cell_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("y3w4M2Tzsb7xZDJJ0000")
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("y3w4M2Tzsb7xZDJJ") # 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 y3w4M2Tzsb7xZDJJ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/y3w4M2Tzsb7xZDJJ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid y3w4M2Tzsb7xZDJJLicense: CC0 1.0
Metadata
- Technology
- Imaging Mass Cytometry
- Organism
- human
- Tissue
- kidney
- Condition
- acute tubulointerstitial nephritis
- Modality
- protein
- Observations (cells)
- 23,985
- Tier
- bronze
- Chemistry
- IMC
- Staining
- Antibodies
- Size
- 132 MB
- Sample ID
- S-BIAD3694:discovery:Batch9:AIN-01-0135: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