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Piccinini F, Tazzari M, Tumedei MM, Stellato M, Remondini D, Giampieri E, Martinelli G, Castellani G, Carbonaro A. Data Science for Health Image Alignment: A User-Friendly Open-Source ImageJ/Fiji Plugin for Aligning Multimodality/Immunohistochemistry/Immunofluorescence 2D Microscopy Images. SENSORS (BASEL, SWITZERLAND) 2024; 24:451. [PMID: 38257548 PMCID: PMC10819694 DOI: 10.3390/s24020451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/30/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Most of the time, the deep analysis of a biological sample requires the acquisition of images at different time points, using different modalities and/or different stainings. This information gives morphological, functional, and physiological insights, but the acquired images must be aligned to be able to proceed with the co-localisation analysis. Practically speaking, according to Aristotle's principle, "The whole is greater than the sum of its parts", multi-modal image registration is a challenging task that involves fusing complementary signals. In the past few years, several methods for image registration have been described in the literature, but unfortunately, there is not one method that works for all applications. In addition, there is currently no user-friendly solution for aligning images that does not require any computer skills. In this work, DS4H Image Alignment (DS4H-IA), an open-source ImageJ/Fiji plugin for aligning multimodality, immunohistochemistry (IHC), and/or immunofluorescence (IF) 2D microscopy images, designed with the goal of being extremely easy to use, is described. All of the available solutions for aligning 2D microscopy images have also been revised. The DS4H-IA source code; standalone applications for MAC, Linux, and Windows; video tutorials; manual documentation; and sample datasets are publicly available.
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Affiliation(s)
- Filippo Piccinini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, FC, Italy; (M.T.); (M.M.T.); (G.M.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, BO, Italy; (E.G.); (G.C.)
| | - Marcella Tazzari
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, FC, Italy; (M.T.); (M.M.T.); (G.M.)
| | - Maria Maddalena Tumedei
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, FC, Italy; (M.T.); (M.M.T.); (G.M.)
| | - Mariachiara Stellato
- Department of Physics and Astronomy “Augusto Righi” (DIFA), University of Bologna, 40127 Bologna, BO, Italy; (M.S.); (D.R.)
| | - Daniel Remondini
- Department of Physics and Astronomy “Augusto Righi” (DIFA), University of Bologna, 40127 Bologna, BO, Italy; (M.S.); (D.R.)
| | - Enrico Giampieri
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, BO, Italy; (E.G.); (G.C.)
| | - Giovanni Martinelli
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, FC, Italy; (M.T.); (M.M.T.); (G.M.)
| | - Gastone Castellani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, BO, Italy; (E.G.); (G.C.)
| | - Antonella Carbonaro
- Department of Computer Science and Engineering (DISI), University of Bologna, 47521 Cesena, FC, Italy;
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