MIBI-TOF
Human brain
S-BIAD1579:CHOP_907_R4C9
bronze glioma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'immune_CHOP_907_R4C9_image': DataTree[cyx] (49, 1024, 1024), (49, 512, 512), (49, 256, 256), (49, 128, 128), (49, 64, 64)
├── Labels
│ ├── 'immune_CHOP_907_R4C9_nuclear_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
│ └── 'immune_CHOP_907_R4C9_whole_cell_labels': DataTree[yx] (1024, 1024), (512, 512), (256, 256), (128, 128), (64, 64)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1085, 2) (2D shapes)
│ └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (1085, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1085, 49)
with coordinate systems:
▸ 'global', with elements:
immune_CHOP_907_R4C9_image (Images), immune_CHOP_907_R4C9_nuclear_labels (Labels), immune_CHOP_907_R4C9_whole_cell_labels (Labels), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("pbdI5ruO717UMEpd0000")
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("pbdI5ruO717UMEpd") # 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 pbdI5ruO717UMEpd0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pbdI5ruO717UMEpd
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pbdI5ruO717UMEpdLicense: CC0 1.0
Metadata
- Technology
- MIBI-TOF
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- protein
- Observations (cells)
- 1,085
- Tier
- bronze
- Chemistry
- MIBI
- Staining
- Antibodies
- Size
- 118 MB
- Sample ID
- S-BIAD1579:CHOP_907_R4C9
- 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