We present Icy2.0 (http://icy.bioimageanalysis.org), which is a major evolution of our previous free and open software for bioimage analysis Icy. This release has three important features: 1) the ability to handle very large images (> 4Gb); 2) the possibility to process long sequences through an optimized streaming procedure with adaptive caching; and 3) a totally redesigned web site for improved interactions within the Icy community. Icy2.0 has retained and consolidated the major features that made its success in the bioimaging community, namely to make it available to the bioimaging community an image analysis software suite that encompasses the large variety of biological applications (microscopy, particle tracking, HCS/HTS, digital pathology, animal behavior…) and users (biologist, bioimage analyst, physicist, developer) and to give access to advanced image analysis methods and solutions.
Since its launching, it has been the constant philosophy of the Icy team to promote sharing of source code and know-how and to facilitate the use of quantitative approaches and open new scientific perspectives in terms of exhaustiveness, reproducibility and robustness of the analysis of bioimaging data sets. For those reasons, Icy2.0 has a fully redesigned web-site, that includes new communication channels between the end-users and the developers, new tutorial material and improved maintenance cycles. Icy2.0 now provides more than 400 dedicated plugins covering a large variety of state-of-the-art image analysis methods ranging from active contours models to Machine Learning through statistical spatial analysis, which empower users with the most recent and adapted quantitative image analysis and visualization tools. Protocols, which are a graphical front-end that enable software development without any programming knowledge, have also been improved and now include the possibility to develop sophisticated image processing pipelines in a more readable and interactive manner.
Icy2.0 has a large community of developers and users (4000+ regular users, 700+ students trained, 1500+ visits per month) that are using Icy for distributing their algorithms and plugins. For its long-term sustainability and development, the Icy2.0 project benefits from the institutional support of the French national Infrastructure FranceBioImaging and of Institut Pasteur. Ongoing work aims at improving the interoperability and convergence of Icy2.0 with other open and free image analysis packages as well as facilitating the integration and use of AI packages.
