FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology

Samuel P. Border, Ricardo Melo Ferreira, Nicholas Lucarelli, Suhas Katari Chaluva Kumar, Anindya S. Paul, David Manthey, Laura Barisoni, Yulia A. Levites Strekalova, Jessica Ray, Ying-Hua Cheng, Avi Z. Rosenberg, John E. Tomaszewski, Sayat Mimar, Jeffrey B. Hodgin, John W. Hickey, Bei Wei, Fiona Ginty, Arivarasan Karunamurthy, Juexin Wang, Mauminah Raina, Gloria S. Pryhuber, Jeffrey Purkerson, Tarek M. El-Achkar (), Sanjay Jain (), Michael T. Eadon () and Pinaki Sarder ()
Additional contact information
Samuel P. Border: University of Florida
Ricardo Melo Ferreira: Indiana University School of Medicine
Nicholas Lucarelli: University of Florida
Suhas Katari Chaluva Kumar: University of Florida
Anindya S. Paul: University of Florida
David Manthey: Inc
Laura Barisoni: Duke University
Yulia A. Levites Strekalova: University of Florida
Jessica Ray: University of Florida
Ying-Hua Cheng: Indiana University School of Medicine
Avi Z. Rosenberg: Johns Hopkins University School of Medicine
John E. Tomaszewski: State University of New York
Sayat Mimar: University of Florida
Jeffrey B. Hodgin: University of Michigan
John W. Hickey: Duke University
Bei Wei: Stanford School of Medicine
Fiona Ginty: GE HealthCare Technology and Innovation Center
Arivarasan Karunamurthy: University of Pittsburgh
Juexin Wang: Indiana University Indianapolis
Mauminah Raina: Indiana University Indianapolis
Gloria S. Pryhuber: University of Rochester
Jeffrey Purkerson: University of Rochester
Tarek M. El-Achkar: Indiana University School of Medicine
Sanjay Jain: Washington University School of Medicine
Michael T. Eadon: Indiana University School of Medicine
Pinaki Sarder: University of Florida

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-63050-9 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63050-9

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-63050-9

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().