TY - JOUR
T1 - FUSION
T2 - a web-based application for in-depth exploration of multi-omics data with brightfield histology
AU - HuBMAP consortium
AU - Border, Samuel P.
AU - Ferreira, Ricardo Melo
AU - Lucarelli, Nicholas
AU - Kumar, Suhas Katari Chaluva
AU - Paul, Anindya S.
AU - Manthey, David
AU - Barisoni, Laura
AU - Levites Strekalova, Yulia A.
AU - Ray, Jessica
AU - Cheng, Ying Hua
AU - Rosenberg, Avi Z.
AU - Tomaszewski, John E.
AU - Mimar, Sayat
AU - Hodgin, Jeffrey B.
AU - Hickey, John W.
AU - Wei, Bei
AU - Ginty, Fiona
AU - Karunamurthy, Arivarasan
AU - Wang, Juexin
AU - Raina, Mauminah
AU - Pryhuber, Gloria S.
AU - Purkerson, Jeffrey
AU - El-Achkar, Tarek M.
AU - Jain, Sanjay
AU - Eadon, Michael T.
AU - Sarder, Pinaki
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/12
Y1 - 2025/12
N2 - Spatial technologies examining the cell and tissue microenvironment at near single-cell resolution are revealing important molecular insights. However, few tools enable integrated, interactive analysis of spatial-omics with tissue morphology in the same functional tissue unit. Here, we present FUSION (Functional Unit State Identification in Whole Slide Images), a web-based platform for visualizing and analyzing spatial-omics data with high-resolution histology. FUSION provides workflows for assessing cell compositions, quantitative morphometrics, and comparative tissue analyses. We demonstrate applicability across spatial assays, including 10x Visium, Visium HD, 10x Xenium, Cell DIVE, and PhenoCycler, applied to healthy and diseased tissues from kidney, small intestine, lung, and skin in the Human BioMolecular Atlas Program. FUSION is cloud-based, open-source, and accessible at https://fusion.hubmapconsortium.org/, hosting over 50 paired datasets and tutorials. In a series of use cases, we show its capacity to distinguish renal glomeruli injury states, quantify morphometric changes, and characterize fibrosis with immune infiltration.
AB - Spatial technologies examining the cell and tissue microenvironment at near single-cell resolution are revealing important molecular insights. However, few tools enable integrated, interactive analysis of spatial-omics with tissue morphology in the same functional tissue unit. Here, we present FUSION (Functional Unit State Identification in Whole Slide Images), a web-based platform for visualizing and analyzing spatial-omics data with high-resolution histology. FUSION provides workflows for assessing cell compositions, quantitative morphometrics, and comparative tissue analyses. We demonstrate applicability across spatial assays, including 10x Visium, Visium HD, 10x Xenium, Cell DIVE, and PhenoCycler, applied to healthy and diseased tissues from kidney, small intestine, lung, and skin in the Human BioMolecular Atlas Program. FUSION is cloud-based, open-source, and accessible at https://fusion.hubmapconsortium.org/, hosting over 50 paired datasets and tutorials. In a series of use cases, we show its capacity to distinguish renal glomeruli injury states, quantify morphometric changes, and characterize fibrosis with immune infiltration.
UR - https://www.scopus.com/pages/publications/105017185992
U2 - 10.1038/s41467-025-63050-9
DO - 10.1038/s41467-025-63050-9
M3 - Article
C2 - 40998789
AN - SCOPUS:105017185992
SN - 2041-1723
VL - 16
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 8388
ER -