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The understanding of multilevel mechanisms, with all the complexity they have from a basic and disease-oriented perspective, is a major challenge and will mobilize a large part of biomedical research in the future. The study of protein and cell assemblies, in such conditions that their intricated cascades of behaviors will be preserved, can not only bring answers to biological and medical questions but also lead to unsuspected issues. Image analysis, applied to joint observations at nanometer to millimeter scales, with its potential to extract and quantify structures and shapes and to track proteins and cells, should bring new insights on mechanisms of life. Significant breakthroughs at experimental and methodological levels are still required to achieve this goal. From an image-processing viewpoint, there is a demand for fully innovative algorithms that will be independent of image intensity variations, shape and topology changes, and any priors on movements. Cutting-edge technologies for in-vivo explorations (e.g., the only natural environment), beyond the endo-microscopes already available, will merge with the image-guided world developed in computer-assisted medicine.