PhenoCycler

Human pancreas

S-BIAD859:6371v1:reg002

silver Interactive viewer type 1 diabetes mellitus ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'reg002_image': DataTree[cyx] (84, 3528, 3360), (84, 1764, 1680), (84, 882, 840), (84, 441, 420), (84, 220, 210)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (57248, 1) (2D shapes)
│     └── 'cell_boundaries_for_vitessce': GeoDataFrame shape: (57248, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (57248, 84)
with coordinate systems:
    ▸ 'global', with elements:
        reg002_image (Images), cell_boundaries (Shapes), cell_boundaries_for_vitessce (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("GYWbIB2mJ2hSKHvK0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("GYWbIB2mJ2hSKHvK")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download GYWbIB2mJ2hSKHvK0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/GYWbIB2mJ2hSKHvK

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid GYWbIB2mJ2hSKHvK

Install (Python 3.12+) Docs →

License: CC0 1.0

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

bia-s-biad859→

2 datasets · publication

Metadata

Technology: PhenoCycler
Organism: human
Tissue: pancreas
Condition: type 1 diabetes mellitus
Modality: protein
Observations (cells): 57,248
Tier: silver
Chemistry: CODEX Processor
Staining: IF
Size: 2.1 GB
Sample ID: S-BIAD859:6371v1:reg002
License: CC0 1.0
Published: Dec 1, 2023

Cite this dataset

doi.org/10.7554/elife.100535 ↗

BibTeX

@article{Barlow_2025,
  title = {The extra-islet pancreas supports autoimmunity in human type 1 diabetes},
  volume = {13},
  ISSN = {2050-084X},
  url = {http://dx.doi.org/10.7554/elife.100535},
  DOI = {10.7554/elife.100535},
  journal = {eLife},
  publisher = {eLife Sciences Publications, Ltd},
  author = {Barlow, Graham L and Schürch, Christian M and Bhate, Salil S and Phillips, Darci J and Young, Arabella and Dong, Shen and Martinez, Hunter A and Kaber, Gernot and Nagy, Nadine and Ramachandran, Sasvath and Meng, Janet and Korpos, Eva and Bluestone, Jeffrey A and Nolan, Garry P and Bollyky, Paul L},
  year = {2025},
  month = Apr
}

Source: BioImage Archive ↗ · License: CC0 1.0 ↗ · Reprocessed to SpatialData by SpatialData-DB