ArticleBioinformatics (Oxford, England)2025
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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15 authors.
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Abstract
motivationTyramide-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.
resultsIntegrAlign, 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 (∼6 µm), 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.
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