IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment

doi:10.1093/bioinformatics/btaf567

IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment

2025-11-01

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OA

AI

Stéphanie Tissot-Renaud

S

Sylvie Rusakiewicz

M

Marie‐Cécile Michallet

N

Nathalie Bendriss‐Vermare

J

Jenny Valladeau‐Guilemond

DOI：10.1093/bioinformatics/btaf567

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Motivation Tyramide-based multiplex-immunofluorescence (mIF) enables the simultaneous analysis of up to seven protein markers on a whole slide, providing a comprehensive approach to study the tumor microenvironment. Integrating multiple mIF panels through image alignment of serial slide significantly expands the number of cell populations analysed in a single space. IntegrAlign was developed to optimize this integration on serial whole slides, enhancing the value and applicability of -mIF for comprehensive spatial analyses and enabling biomarker discovery at scale.Results IntegrAlign, leveraging the SimpleITK toolkit, applies a two-step alignment using rigid and B-spline transformations to integrate serial mIF whole slides. Validation on simulated and real datasets demonstrated alignment accuracy below the diameter of a cell nucleus (similar to 6 mu m), outperforming existing methods. This precision enhances spatial analyses by combining extended phenotypic data, supporting novel insights into tissue architecture and cellular interactions.Availability and implemention IntegrAlign is open-source, implemented in Python, and freely available under the MIT license at https://github.com/CAUXlab/IntegrAlign.

IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment

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