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Advanced BiomEdical OPTICAL Imaging and Data Analysis

Periodic Reporting for period 2 - BE-OPTICAL (Advanced BiomEdical OPTICAL Imaging and Data Analysis)

Reporting period: 2017-10-01 to 2019-09-30

Biomedical imaging is a research field that is producing ground breaking scientific discoveries that enhance the health and life quality of European citizens and have a huge economic impact. In order to maintain Europe’s leading position in the field, it is crucial to invest in the people who will lead research and development, and to promote the academic-private sector partnerships that will transfer the novel technologies to the market.

By training a new generation of researchers, by developing cutting-edge science, and by engaging in long-term collaborations, BE-OPTICAL will not only strengthen the European position in the field of biomedical imaging, but it will also bring direct societal returns through improved health care services.

The main objective of the BE-OPTICAL project is to provide top-class multi-skill training to 14 early stage researchers on optical imaging techniques (super-resolution fluoresce microscopy, high-resolution cardiac imaging, ophthalmic imaging), and on optical components and image data analysis methods.
Organized training events

Two schools, four workshops and several short training modules have been organized. The training materials are available at

Work carried by Work Package

Work Package 1: Super-resolution optical imaging for the analysis of cellular processes

This research topic involves the work of three early stage researchers.

Soheil Mojiri (early stage researcher 1 at Georg August University, Germany) developed a multi-plane phase contrast 3D imaging system using super-resolution optical fluctuation imaging and light sheet fluorescence microscopy.

Adrià Escobet (early stage researcher 2 at University of St. Andrews, UK) research developed a new technology that allows imaging microscopic fluorescent samples through hundreds of microns of turbid media and tissue without aberration correction.

Mariano Gonzalez Pisfil (early stage researcher 3 at PicoQuant, Germany) developed a time-resolved imaging technique to track multi-stained samples in super-resolution microscopy.

Work package 2: High-resolution optical imaging of cardiac tissue

This research topic involves the work of four early stage researchers.

Vineesh Kappadan (early stage researcher 4 at the Max Plank Institute, Germany) developed new algorithms for removing motion artifacts during simultaneously recording of the electrical and mechanical activity of heart using fluorescent imaging technique.

Raul Quiñonez Uribe (early stage researcher 5, also at the Max Plank Institute, Germany) developed a fluorescence imaging system for contracting intact heart using optogenetics.

Setegn Ayalew (early stage researcher 6 at the University of Glasgow, UK) original research project was not implemented (because the researcher left the project) but the research was re-defined using software instead of hardware and additional data analysis algorithms were developed (work performed by researcher 14, Pablo Amil based at Universitat Politecnica de Catalunya, Spain).

Michał Hamkało (early stage researcher 7 at Nicolas Copernicus University, Poland) developed a system for imaging through turbid media using wavefront modulated illumination and full-field optical coherence microscopy.

Work package 3: Advanced instrumentation for ophthalmic imaging

This research topic involves the work of three early stage researchers.

Tommaso Alterini (early stage researcher 8 at Universitat Politecnica de Catalunya, Spain) developed of a novel LED-based hyperspectral imaging system to image spatial and spectral properties of the ocular fundus.

Ana Rodriguez (early stage researcher 9 at the Institute de Microcirugia Ocular, Spain) developed a prototype of an optoelectronic instrument for visual performance diagnosis that incorporates an optical coherence tomography system that permits the anterior segment imaging modality and a retinal imaging modality.

Alfonso Jiménez (early stage researcher 10 at Nicolas Copernicus University, Poland) developed an optical coherence tomography-based ocular biometer that, combined with an air-puff system, allows for retraction-free investigation of the eye dynamics.

Work package 4: Innovative optical components, methods and software for image analysis

This transversal work package is aimed at developing optical and analysis tools that are specifically designed for optimising the images obtained with the techniques developed in the other work packages. It involves the work of four early stage researchers.

Donatus Halpaap (early stage researcher 11 at Universitat Politecnica de Catalunya, Spain) investigated the speckle generated by various light sources and demonstrated that speckle (relevant for double pass retina imaging) can be mitigated by using a laser pumped near threshold and adjusting the CCD camera adquisition settings.

Antu Nehuen Gortari (early stage researcher 12 at the Centre National de la Recherche Scientifique, France) developed novel nano-engineered substrates to enhance the resolution of microscopy techniques. The metasurfaces were integrated in a prototype of a total internal reflection microscope.

Shun Qin (early stage researcher 13 at Georg August University, Germany) developed novel image deconvolution techniques for super-resolution microscopy.

Pablo Amil (early stage researcher 14 at Universitat Politecnica de Catalunya, Spain) developed novel machine learning methods for the characterization and the classification of complex data (for ordering optical coherence tomography anterior chamber images, for classification of retinal fundus images, and for the detection of images with artifacts in large databases).
The project has developed several prototypes of novel imaging instruments, has developed novel substractes and light sources for imaging, and novel data analysis methods and algorithms. Two PhD thesis have been completed (links are available in the project web page) and several more thesis are expected for the next few months. One patent has been granted (for OCT image classification) and two more are expected (outlier detection methods and nano-engineered substrates) within the next few months. Present efforts are focused on identifying companies interested in commercializing the new developed techniques.