IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment
Leo Hermet, Leo Laoubi, Martial Scavino, Anne-Claire Doffin, Alexia Gazeu, Justine Berthet, Berenice Pillat, Stephanie Tissot, Sylvie Rusakiewicz, Marie‐Cécile Michallet, Nathalie Bendriss-Vermare, Jenny Valladeau-Guilemond, Jean Hausser, Christophe Caux, Margaux Hubert
TL;DR
IntegrAlign is a new tool that aligns multiple immunofluorescence images to study tissue structures and cell interactions with high precision.
Contribution
IntegrAlign introduces a precise two-step image alignment method for multi-immunofluorescence panels, improving spatial analysis accuracy.
Findings
IntegrAlign achieves alignment accuracy below 6 µm, outperforming existing methods.
The tool supports combining extended phenotypic data from serial whole slides for spatial analysis.
It is open-source and validated on both simulated and real datasets.
Abstract
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. 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 (∼6 µm), outperforming existing methods. This precision enhances…
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Taxonomy
TopicsSingle-cell and spatial transcriptomics · Glycosylation and Glycoproteins Research · Advanced Biosensing Techniques and Applications