We have succeeded in going beyond the state of the art as described in the initial project in the following orientations:
• New labels to image in vivo processes either during development or during infectious processes have been developed or implemented to study either mammalian or zebrafish early development. This has been the main topic of D1.3” In vivo tracers, reporters & actuators”, and partially that of D1.4 “New protocols to image the developing vertebrate embryos to the subcellular level”. The main progresses within ImageInLife have been related to innovative strategies to label specific cell populations or ongoing processes.
• New to tools to image biological processes in vivo, microscopes and incubation chambers have been developed by ESRs 10 and 14 and their respective beneficiary institutions. This has been the main topic of D2.1 “Incubation chambers”, D2.2 “Multimodal and multiscale LSFM workstation”, MS20 “Effective Super-Resolution imaging”, MS23 “VAST BioImager”, D2.3 “Super-resolution-LSFM for imaging of cellular processes within the embryo” and D2.4 “Image acquisition systems for infected embryos”. The development of new imaging chambers has been critical for the progress of the project, and together with new imaging strategies have yielded impressive results.
• New mathematical tools to analyse 3D or 4D image datasets have been the main topic of D3.1 “Design of image processing and analysis methods”, D3.2 “Computer implementation of image processing and analysis methods” and D3.3 “Application of image processing and analysis methods to ImageInLife data”
• New tools to model development and morphogenesis have been the main topic of D4.1 “Cell biomechanics”, D4.2 “Tissue geometry & physics”, and D4.5 “Search & optimisation”.
• New image processing solutions for high-content screenings using vertebrate embryos have been one of the main topic of D3.2 “Computer implementation of image processing and analysis methods”, and D3.3 “Application of image processing and analysis methods to ImageInLife data”.
• Implementation of these results in medical image processing software as it will bring the results of the network to the clinics for better diagnosis and choice of treatments. This has been the other main topic of D3.2 “Computer implementation of image processing and analysis methods”, and D3.3 “Application of image processing and analysis methods to ImageInLife data”.
The four last topics, at the heart of the transdisciplinary nature of ImageInLife, required close collaboration between wet biologists, mathematicians, physicists and computer scientists, have been very productive and critical to open the mind of the ESRs to the transdisciplinarity of their future research positions.
This transdisciplinarity of ImageInLife led to the production of both classical scientific articles published on line, and to the development of software packages publicly released on the ImageInLife community page on zenodo.org under open-source licences. They all have been developed with the contribution of at least one of the beneficiary private companies of ImageInLife, and we consider that this part of the project involving two very active private companies, Acquifer and TatraMed is a real success. These packages include the ImageInLib image processing library created by ESR13 in the frame of a collaboration between the ImageInLife teams from TatraMed Software s.r.o and Slovak University of Technology, and numerous tools developed by ESR12 from Acquifer for automatic object recognition on 4D images, stack projections, hyperstack manipulations, qualitative annotations and image classifications (see Milestone 28).
