High-Resolution Multi-Spectral Imaging With Diffractive Lenses and Learned Reconstruction

Spectral imaging is a fundamental diagnostic technique with widespread application. Conventional spectral imaging approaches have intrinsic limitations on spatial and spectral resolutions due to the physical components they rely on. To overcome these physical limitations, in this paper, we develop a novel multi-spectral imaging modality that enables higher spatial and spectral resolutions. In the developed computational imaging modality, we exploit a diffractive lens, such as a photon sieve, for both dispersing and focusing the optical field, and achieve measurement diversity by changing the focusing behavior of this lens. Because the focal length of a diffractive lens is wavelength-dependent, each measurement is a superposition of differently blurred spectral components. To reconstruct the individual spectral images from these superimposed and blurred measurements, model-based fast reconstruction algorithms are developed with deep and analytical priors using alternating minimization and unrolling. Finally, the effectiveness and performance of the developed technique is illustrated for an application in astrophysical imaging under various observation scenarios in the extreme ultraviolet (EUV) regime. The results demonstrate that the technique provides not only diffraction-limited high spatial resolution, as enabled by diffractive lenses, but also the capability of resolving close-by spectral sources that would not otherwise be possible with the existing techniques. This work enables high resolution multi-spectral imaging with low cost designs for a variety of applications and spectral regimes.

Coherent imaging from bacteria to multicellular organisms

Séverine Coquoz

Structural and functional imaging of cells, tissues and organisms is crucial for understanding biomedical processes. Fluorescence microscopy is an established tool and has contributed to many discoveries in the life sciences. This technique provides molecular contrast but has limitations inherent to the fluorescent probes, namely phototoxicity and photobleaching. Phase microscopy provides a label-free alternative. Contrast is achieved by translating the phase variations induced by the sample into measurable intensity variations. While phase contrast and differential interference contrast microscopy offer a means to generate contrast without exogenous contrast agents, quantitative phase imaging (QPI) techniques have emerged, enabling the measurement of the phase delays. This measurement yields information on the thickness, refractive index and dry mass of the sample. QPI is thus a powerful tool and has proven its use in various biomedical applications. In the first part of this thesis, new concepts for extending the capabilities of QPI and applications exploiting them are presented. We implement piezo-based Fourier phase microscopy, exhibiting high spatial and temporal sensitivities and resolutions for label-free imaging of cell dynamics at various time scales. The phase is retrieved via phase-shifting intereferometry using a piezo-actuated module allowing very fast tunable phase modulation. Several examples of applications are described. Furthermore, we exploit the phase-to-mass equivalence for investigating the growth of uropathogenic E. coli and the effect of different antibiotics, thereby providing new insights into fundamental mechanisms of bacterial growth. Because QPI methods are limited to optically thin and weakly scattering objects, the second part of this thesis focuses on optical coherence microscopy (OCM). OCM is an interferometric technique providing 3D images of highly scattering biological samples with micrometric resolution and penetration depth of up to several hundreds of micrometers. Compared to optical coherence tomography, OCM uses high numerical aperture (NA) optics to achieve higher transverse resolution, leading to a decrease of the depth of field (DOF). Several methods have been developed to overcome this trade-off between resolution and DOF. Extended-focus OCM (xfOCM) provides a particularly interesting solution by illuminating the sample with a Bessel beam. Moreover, interferometric synthetic aperture microscopy (ISAM) achieves depth-independent resolution through an approximate solution to the inverse scattering problem. We develop extended ISAM (xISAM) to combine the benefits of both approaches, and demonstrate its potential on simulated and experimental data. We also propose a new application of visible OCM (visOCM), a xfOCM system using visible light and a high-NA objective to achieve 3D imaging with sub-micrometer spatial resolution. The capabilities of visOCM are well suited for 3D in vivo imaging of C. elegans, an extensively used model organism in biomedical research. We demonstrate that the anatomy of C. elegans can be visualized with high speed and high contrast down to the sub-cellular level. We further show that visOCM can be employed for imaging age-related morphological changes. Altogether, the methods developed in this thesis pave the way to many applications in the life sciences by featuring label-free imaging at various temporal and spatial scales. Several promising applications are pursued.

EPFL2017

Coherent imaging from bacteria to multicellular organisms

Séverine Coquoz

EPFL2017