from sddb import Catalog
cohort = Catalog().collection("bia-s-biad859")
cohort.members # the 2 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")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")
coll = db.Collection.get(key="bia-s-biad859")
coll.ordered_artifacts.to_dataframe() # the 2 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection bia-s-biad859 --dest data/Licenses: 2 CC0 1.0
In autoimmune type 1 diabetes (T1D), immune cells infiltrate and destroy the islets of Langerhans - islands of endocrine tissue dispersed throughout the pancreas. However, the contribution of cellular programs outside islets to insulitis is unclear. Here, using CO-Detection by indEXing (CODEX) tissue imaging and cadaveric pancreas samples, we simultaneously examine islet and extra-islet inflammation in human T1D. We identify four sub-states of inflamed islets characterized by the activation profiles of CD8<sup>+</sup>T cells enriched in islets relative to the surrounding tissue. We further find that the extra-islet space of lobules with extensive islet-infiltration differs from the extra-islet space of less infiltrated areas within the same tissue section. Finally, we identify lymphoid structures away from islets enriched in CD45RA<sup>+</sup> T cells - a population also enriched in one of the inflamed islet sub-states. Together, these data help define the coordination between islets and the extra-islet pancreas in the pathogenesis of human T1D.
@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
}