{"entity": "publication", "iuid": "3d8d5a4603a54c3d9021f52942d0a5fb", "timestamp": "2026-08-20T20:36:20.754Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d8d5a4603a54c3d9021f52942d0a5fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d8d5a4603a54c3d9021f52942d0a5fb"}}, "title": "IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment.", "authors": [{"family": "Hermet", "given": "Leo", "initials": "L"}, {"family": "Laoubi", "given": "Leo", "initials": "L", "orcid": "0000-0001-9388-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2aee7102f954b9982fe0bd0e2c86663.json"}}, {"family": "Scavino", "given": "Martial", "initials": "M"}, {"family": "Doffin", "given": "Anne-Claire", "initials": "AC"}, {"family": "Gazeu", "given": "Alexia", "initials": "A"}, {"family": "Berthet", "given": "Justine", "initials": "J"}, {"family": "Pillat", "given": "Berenice", "initials": "B"}, {"family": "Tissot", "given": "Stephanie", "initials": "S"}, {"family": "Rusakiewicz", "given": "Sylvie", "initials": "S"}, {"family": "Michallet", "given": "Marie-C\u00e9cile", "initials": "MC"}, {"family": "Bendriss-Vermare", "given": "Nathalie", "initials": "N"}, {"family": "Valladeau-Guilemond", "given": "Jenny", "initials": "J"}, {"family": "Hausser", "given": "Jean", "initials": "J"}, {"family": "Caux", "given": "Christophe", "initials": "C"}, {"family": "Hubert", "given": "Margaux", "initials": "M", "orcid": "0000-0003-2584-6494", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/25a4d71202cb4f1b8e98b9f76768f210.json"}}], "type": "journal article", "published": "2025-11-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "41", "issue": "11", "issn-l": "1367-4803"}, "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.\n\nIntegrAlign, 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 (\u223c6 \u00b5m), outperforming existing methods. This precision enhances spatial analyses by combining extended phenotypic data, supporting novel insights into tissue architecture and cellular interactions.\n\nIntegrAlign is open-source, implemented in Python, and freely available under the MIT license at https://github.com/CAUXlab/IntegrAlign.", "doi": "10.1093/bioinformatics/btaf567", "pmid": "41100186", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12582367"}, {"db": "pii", "key": "8287766"}], "notes": [], "created": "2026-08-20T09:40:04.990Z", "modified": "2026-08-20T09:40:05.123Z"}