Abstract
Wavefront sensors (WFSs) encode phase information of an incoming wavefront into an intensity pattern that can be measured on a camera. Several kinds of WFSs are used in astronomical adaptive optics. Among them, Fourier-based WFSs perform a filtering operation on the wavefront in the focal plane. The most well-known example of a WFS of this kind is the Zernike WFS. The pyramid WFS also belongs to this class. Based on this same principle, WFSs can be proposed, such as the n-faced pyramid (which ultimately becomes an axicon) or the flattened pyramid, depending on whether the image formation is incoherent or coherent. To test such concepts, the LAM/ONERA on-sky pyramid sensor (LOOPS) adaptive optics testbed hosted at the Laboratoire d'Astrophysique de Marseille has been upgraded by adding a spatial light modulator (SLM). This device, placed in a focal plane produces high-definition phase masks that mimic otherwise bulk optic devices. We first present the optical design and upgrades made to the experimental setup of the LOOPS bench. Then, we focus on the generation of the phase masks with the SLM and the implications of having such a device in a focal plane. Finally, we present the first closed-loop results in either static or dynamic mode with different WFS applied on the SLM.

Abstract
For extremely large telescopes, adaptive optics will be required to correct the Earth’s turbulent atmosphere. The performance of tomographic adaptive optics is strongly dependent on the vertical distribution (profile) of this turbulence. An important way in which this manifests is the tomographic error, arising from imperfect measurement and reconstruction of the turbulent phase at altitude. Conventionally, a small number of reference profiles are used to obtain this error in simulation; however these profiles are not constructed to be representative in terms of tomographic error. It is therefore unknown whether these simulations are providing realistic performance estimates. Here, we employ analytical adaptive optics simulation that drastically reduces computation times to compute tomographic error for 10 691 measurements of the turbulence profile gathered by the Stereo-SCIDAR instrument at ESO Paranal. We assess for the first time the impact of the profile on tomographic error in a statistical manner. We find, in agreement with previous work, that the tomographic error is most directly linked with the distribution of turbulence into discrete, stratified layers. Reference profiles are found to provide mostly higher tomographic error than expected, which we attribute to the fact that these profiles are primarily composed of averages of many measurements resulting in unrealistic, continuous distributions of turbulence. We propose that a representative profile should be defined with respect to a particular system, and that as such simulations with a large statistical sample of profiles must be an important step in the design process.

Abstract
Imaging methods are a powerful tool for diagnostic purposes. In this chapter, the most important light-imaging methods, their advantages, and drawbacks are described. The advantages of radiation-free light-based imaging methods relative to traditional radiation methods, such as X-ray, magnetic resonance, or positron emission imaging, are indicated, and the recent advances to improve probing depth, contrast, and resolution in thick tissues are demonstrated. Some historical aspects and recent improvements in light-imaging methods, such as optical coherence tomography, speckle-imaging, second harmonic generation, or light-sheet microscopies, are presented. Due to the recent combination of optical immersion clearing with light-based imaging methods, several studies have been reported, where high-quality images and 3D reconstruction have been obtained for various tissues, providing an alternative to traditional histology or histopathology methods. The purpose of optical clearing is to reduce light scattering, but tissue clearing is obtained through three mechanisms: tissue dehydration, refractive index matching, and protein dissociation. This last mechanism leads to a reduction in the intensity of protein fluorescence, which can be a disadvantage in fluorescence imaging methods. The selection of certain clearing protocols that minimizes or eliminates protein dissociation has been made by some researchers, and a review of such literature is made in the various sections of this chapter.

Abstract
There are several types of measurements that can be performed with biological tissues during optical clearing treatments. When analyzing these methods, two major modes of study must be provided: ex vivo and in vivo. Measurements made from ex vivo samples are more flexible, allowing, for instance, to measure tissue transmittance or sample thickness kinetics. The results obtained from these measurements do not mimic exactly the in vivo situation. In the case of in vivo tissues, results from measurements are more realistic, but a more restrict number is possible, based only on reflectance or imaging methods. In this chapter, we make a brief description and analysis of the various measurement procedures that can be made during treatments of tissues ex vivo and in vivo and present some studies where important information was collected. The valuable results already obtained or possible to obtain in future from measurements described here will be presented and explained in the following sections. A particular case with great interest not only for biophotonics but also for food industry or organ preservation is the estimation of the diffusion properties of water and agents. Such evaluation of parameters is based only on collimated transmittance and thickness measurements made from ex vivo tissues. We will describe these measurements here and exploit their use in the study of diffusion in Chap. 7.

Abstract
[No abstract available]

Abstract
The optical immersion clearing is an effective method to reduce light scattering in tissues, but to optimize each treatment, it is necessary to understand the mechanisms involved. Since these treatments are intended to be temporary, it is also important to know if the mechanisms involved are reversible. Various studies have been made to evaluate and characterize the mechanisms of optical clearing. In all cases studied, two major mechanisms were observed—the tissue dehydration and the refractive index matching mechanisms. Some particular studies have reported that the agents used in treatments also dissolve proteins and suggested that protein dissolution is also a clearing mechanism. All these mechanisms have been reported as reversible, both on ex vivo or on in vivo studies. We make an analysis on these studies and present a method based on ex vivo collimated transmittance and thickness measurements to characterize the major clearing mechanisms—tissue dehydration and refractive index matching. Although this method can only be made with ex vivo tissues, alternative measurements are suggested for in vivo characterization of the clearing mechanisms. © 2019, The Author(s), under exclusive license to Springer Nature Switzerland AG.