High resolution differential laser interferometry for the VLTI (Very Large Telescope Interferometer)

One method for locating extrasolar planets is to observe the lateral movement of a star in the sky caused by a planet in orbit around it. In order to detect this displacement, the angular position of the star has to be measured with high accuracy. This technique is called astrometry. The Very Large Telescope Interferometer (VLTI) is operated by the European Southern Observatory and located at the Paranal Observatory in Chile. The purpose of the PRIMA instrument (Phase Referenced Imaging and Micro-arcsecond Astrometry) of the VLTI is to perform high-resolution astrometric measurements and high-resolution imaging of faint stars using white light interferometry, by combining the light collected by two telescopes. In order to allow the detection of extrasolar planets, the astrometric measurement has to be performed with micro-arcsecond accuracy. In astrometric mode the PRIMA instrument observes two targets at the same time: the object of scientific interest, and a bright reference star. The angular position of the science object relative to the reference star is obtained by monitoring the differential optical path travelled by the light of each object in two separate white-light interferometers. The aim of this work was to develop a high-resolution laser metrology based on superheterodyne interferometry, with an accuracy of 5 nm over a differential optical path of 100 mm. Moreover the laser source had to be stabilised on an absolute frequency reference, in order to ensure the long-term stability and calibration required to achieve the target performance. Superheterodyne interferometry allowed the direct measurement of the differential optical path using two heterodyne interferometers working with two different frequency shifts. The differential phase measurement between the two interferometers was obtained by electronic mixing of the two heterodyne signals, leading to the differential optical path needed for the astrometric measurement

Development of novel experimental and computational methods for three-dimensional coherent and super-resolution microscopy

Adrien Charles-François Raymond Descloux

Optical microscopy is one widely used tool to study cell functions and the interaction of molecules at a sub-cellular level. Optical microscopy techniques can be broadly divided into two categories: partially coherent and incoherent. Coherent microscopy techniques are usually label-free and provide diffraction limited structural information about the sample refractive index distribution though the measurement of phase delay induced by the sample. Since they can be very conservative in the illumination power directed toward the sample, they exhibit very low photo-toxicity and are suitable for both high speed and time lapse imaging. Fluorescence microscopy is an incoherent microscopy method which uses biochemistry techniques to label cellular structures with fluorescent molecules which emit light when excited by a laser. Fluorescence microscopy provides diffraction limited high specificity imaging but is limited in time due to photo-bleaching and photo-toxicity. Super-resolution microscopy is a sub-category of fluorescence microscopy which manipulates and exploits some properties of the fluorescent molecules to achieve high specificity sub-diffraction imaging. Super-resolution comes however at the price of an increased total acquisition time, which limits the applications of super-resolution microscopy to relatively slow cellular processes. The ideal microscope however does not exist; due to the limited spatio-temporal bandwidth of far-field microscopy, there will always be unavoidable trade-offs. There is therefore a need to find new ways to ensure that the methods are reaching their optimal performances and a need to study how different methods can complement each others. I start by presenting a new method for three-dimensional quantitative phase retrieval. I derive a model for the image formation of three-dimensional bright field images and extrapolate a novel expression allowing to retrieve the phase distribution from a bright field image stack. Using a unique image-splitting multi-plane prism that allows to acquire 8 distinct focal planes in a single exposure, I demonstrate three-dimensional quantitative phase imaging at 200 Hz . Finally, I show the association of three-dimensional super-resolution SOFI with phase imaging. To improve the imaging speed and lower the illumination intensity, I combine the same prism platform with a high-speed structured illumination. Since the structured illumination presented is using a digital micro-mirror device, about 90 % of the laser light is diffracted outside of the optical path. To improve the illumination efficiency but keep its speed and flexibility, I present a new approach for achromatic high power high speed SIM, based on a Michelson interferometer. With the access to high illumination power density, I also show the first experimental combination of SIM with SOFI using a self-blinking dye. Motivated by the absence of tools to objectively judge the performance of the microscopy methods I develop, I present a novel algorithm for image resolution estimation. The method estimate the resolution by correlating the image with several filtered version of itself without any external parameters. Finally, in the context of the AD-gut consortium, I show a practical application of deep neural networks used to assists the segmentation and mapping of the microscopy image of enzymatically labeled DNA molecules.

EPFL2020

Compact lensless digital holography

Manon Rostykus

Microscopy is of high interest for biology since it allows imaging features that are too small to be seen with naked eyes. However, cells are mostly transparent to visible and infrared light which makes it difficult to see with a traditional microscope. To do so, phase imaging was invented by F. Zernike, who received the Nobel prize in 1953 for this invention. It provides intensity contrast to visualize transparent samples such as those found in biology without any staining. Among the different implementations of phase imaging, digital holographic microscopy (DHM) is a well-known phase method which provides a quantitative value of the phase generated by the sample under test. Implementations of DHMs without the help of any lens element (so called lensless) offer the added advantage to provide large field of views (severalmm2 compared to several hundred ¹m2) and more compact setups than traditional DHMs which have high quality microscope objectives. The lateral resolution is limited by the pixel size of the camera. However, several techniques have been developed to obtain subpixel resolution with lensless setups, hence giving a resolution smaller than the pixel size. In this thesis, two lensless transmission DHMs are presented using a side illumination technique in order to further reduce the device size and keep a visual access to the sample. The first one operates in an in-line configuration: the most compact but using time-consuming image post-processing. The second one is also lensless and uses an off-axis configuration allowing quasi-real time imaging but less compact. Their practical use is described and images of transparent (phase only) samples are shown. Super-resolution (subpixel) using several subpixel shifted holograms was then investigated for the in-line configuration and demonstrated on absorptive samples. Since those microscopes are compact and made out of off-the-shelf low priced elements, they could be broadly spread in schools for educational purposes. They could also be implemented in cells incubators, allowing visualization inside processes at low cost and multiplication of the number of measurements made at the same time.

EPFL2018

Endoscopic low coherence interferometry applied to tri-dimensional contouring of upper airways

Yves Delacrétaz

This thesis presents a novel approach for optical tri-dimensional contouring, requiring only one acquisition to extract a contour depth. It is based on an interferometric setup, using a reduced coherence light source, and is fully adaptable to endoscopic procedure commonly in used in ear-nose-throat (ENT) medicine. It has been demonstrated that the method can be successfully applied to imaging of porcine upper airways. Although this method uses interferometry to obtain depth range measurement, the phase signal is not directly evaluated, rather the location of the coherent superposition of two waves is extracted, and thus provides a robust technique even in harsh environment. The key feature is to extract the coherent area on the image by locating intentionally induced fringes created by off-axis superposition of a smooth reference wave and an object wave coming from a rough or diffusing sample through an optical system with limited aperture. A model for the propagation of the light through the optical system has been developed. It takes into account the broadened emission spectrum of the light source, as well as the statistical speckle effect induced by the illumination of a rough surface with partially coherent light. Simulated results have been carefully compared with measurements, both in the spatial domain and in the Fourier domain (spatial frequencies response), which has permitted to better understand the processes involved in the creation of the interference fringes, and improve the design of the device. Different filters have been investigated in order to extract the depth information from acquired interferograms. By using Gabor filterbanks, which do not need any a priori knowledge of the signal, selectivity of the extracted signal has been enhanced by a factor of 1.3 compared to a simple local Fourier spectrum evaluation, and time of the extraction procedure divided by 6, even when compared to fast iterative calculation in the Fourier spectrum. Moreover, by imposing the frequency and/or orientation of the signal to detect, which can be known by a simple calibration procedure, it has been proved that the selectivity can be further enhanced by a factor of 2.5, keeping the calculation time as short or even shorter. A compact prototype has been designed and built, with a specific multiple fibers arrangement for illumination. The system is separated in two parts: the first one is directly attached to the rigid endoscope, and contains imaging as well as recombining object/reference wave optics, and the detector. It fits into a box with overall dimensions of 115 × 83 × 94 mm. The second part contains the laser source, the scanning arm and the injection optics for the fibered system. It is designed to be left on a small cart. This device can potentially be brought to the bedside, and used during routine endoscopic check-up. Associated with the device, a complete framework has been elaborated in order to simplify the acquisition procedure as well as the signal processing. This results in a fully automated environment taking in charge hardware control, data storage and signal processing, up to the tri-dimensional scene rendering.

EPFL2009