MIBI-TOF
Human brain
S-BIAD1579:CHOP_941_R6C2:tumor
bronze glioma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'tumor_CHOP_941_R6C2_image': DataTree[cyx] (50, 1024, 1024), (50, 512, 512), (50, 256, 256), (50, 128, 128), (50, 64, 64)
├── Labels
│ ├── 'tumor_CHOP_941_R6C2_nuclear_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│ └── 'tumor_CHOP_941_R6C2_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1200, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (1200, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1200, 50)
with coordinate systems:
▸ 'global', with elements:
tumor_CHOP_941_R6C2_image (Images), tumor_CHOP_941_R6C2_nuclear_labels (Labels), tumor_CHOP_941_R6C2_whole_cell_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("RtaL5vCtpaK8Qlaq0000")
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("RtaL5vCtpaK8Qlaq") # 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 RtaL5vCtpaK8Qlaq0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/RtaL5vCtpaK8Qlaq
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid RtaL5vCtpaK8QlaqLicense: CC0 1.0
Metadata
- Technology
- MIBI-TOF
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- protein
- Observations (cells)
- 1,200
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 115 MB
- Sample ID
- S-BIAD1579:CHOP_941_R6C2:tumor
- License
- CC0 1.0
- Published
- Jan 22, 2025
Cite this dataset
doi.org/10.1016/j.ccell.2025.11.006 ↗ BibTeX
@article{bia:S-BIAD1579,
doi = {10.1016/j.ccell.2025.11.006},
title = {S-BIAD1579:CHOP_907_R98C2}
}Source: BioImage Archive ↗ · License: CC0 1.0 ↗ · Reprocessed to SpatialData by SpatialData-DB