Roadmap on holography

From its inception holography has proven an extremely productive and attractive area of research. While specific technical applications give rise to 'hot topics', and three-dimensional (3D) visualisation comes in and out of fashion, the core principals involved continue to lead to exciting innovations in a wide range of areas. We humbly submit that it is impossible, in any journal document of this type, to fully reflect current and potential activity; however, our valiant contributors have produced a series of documents that go no small way to neatly capture progress across a wide range of core activities. As editors we have attempted to spread our net wide in order to illustrate the breadth of international activity. In relation to this we believe we have been at least partially successful

High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles

Spread-space spread-spectrum technique for secure multiplexing

A novel technique for multiplexing complex images is proposed in which each image may be demultiplexed only if a set of random encryption keys is known. The technique utilizes the ability of the double random phase encoding method to spread a signals’ energy in both the space and the spatial frequency domains in a controlled manner. To multiplex, images are independently encrypted with different phase keys and then superimposed by recording sequentially on the same material. Each image is extracted by using the particular key associated with it. During decryption the energy from the other images is further spread, making it possible to minimize its effects by using suitable filters. Wigner analysis is applied to the technique, and numerical results are presented.Irish Research Council for Science, Engineering and Technologype,la, sp,ke, ab, is, en - kpw6/12/1

Wigner distribution in optics

In 1932 Wigner introduced a distribution function in mechanics that permitted a description of mechanical phenomena in a phase space. Such a Wigner distribution was introduced in optics by Dolin and Walther in the sixties, to relate partial coherence to radiometry. A few years later, the Wigner distribution was introduced in optics again (especially in the area of Fourier optics), and since then, a great number of applications of the Wigner distribution have been reported. While the mechanical phase space is connected to classical mechanics, where the movement of particles is studied, the phase space in optics is connected to geometrical optics, where the propagation of optical rays is considered. And where the position and momentum of a particle are the two important quantities in mechanics, in optics we are interested in the position and the direction of an optical ray. We will see that the Wigner distribution represents an optical field in terms of a ray picture, and that this representation is independent of whether the light is partially coherent or completely coherent. We will observe that a Wigner distribution description is in particular useful when the optical signals and systems can be described by quadratic-phase functions, i.e., when we are in the realm of first-order optics: spherical waves, thin lenses, sections of free space in the paraxial approximation, etc. Although formulated in Fourier-optical terms, the Wigner distribution will form a link to such diverse fields as geometrical optics, ray optics, matrix optics, and radiometry. Sections 1.2 through 1.7 will mainly deal with optical signals and systems. We treat the description of completely coherent and partially coherent light fields in Section 1.2. The Wigner distribution is introduced in Section 1.3 and elucidated with some optical examples. Properties of the Wigner distribution are considered in Section 1.4. In Section 1.5 we restrict ourselves to the one-dimensional case and observe the strong connection of the Wigner distribution to the fractional Fourier transformation and rotations in phase space. The propagation of the Wigner distribution through Luneburg’s first-order optical systems is the topic of Section 1.6, while the propagation of its moments is discussed in Section 1.7. The final Section 1.8 is devoted to the broad class of bilinear signal representations, known as the Cohen class, of which the Wigner distribution is an important representative

A comparison of wavelet analysis techniques in digital holograms

Molony KM, Maycock J, McDonald JB, Hennelly BM, Naughton TJ. A comparison of wavelet analysis techniques in digital holograms. In: SPIE Photon Management III. Vol 6994. SPIE; 2008: 699412

Speckle reduction from digital holograms by simulating temporal incoherence

Hennelly BM, Kelly DP, Maycock J, Naughton TJ, McDonald JB. Speckle reduction from digital holograms by simulating temporal incoherence. In: Applications of Digital Image Processing XXX. Proceedings of SPIE. Vol 6696. San Diego, CA: SPIE; 2007.Speckle is an inherent characteristic of coherent imaging systems. Often, as in the case of Ultrasound, Synthetic Aperture Radar, Laser Imaging and Holography, speckle is a source of noise and degrades the reconstructed image. Various methods exist for the removal of speckle in such images. One method, which has received attention for the removal of speckle from coherent imaging, is to use a temporally incoherent source. We create a novel digital signal processing technique for the reduction of speckle from digital holograms by simulating temporal incoherence during the digital reconstruction process. The method makes use of the discrete implementation of the Fresnel Transform, which calculates the reconstructed image for a range of different wavelengths. These different spectral components can be weighted to suit a temporally incoherent source and the intensities from each wavelength are added together. The method is examined using the speckle index metric

Quantifying the 2.5D imaging performance of digital holographic systems

Digital holographic systems are a class of two step, opto-numerical, three-dimensional imaging techniques. The role of the digital camera in limiting the resolution and field of view of the reconstructed image, and the interaction of these limits with a general optical system is poorly understood. The linear canonical transform describes any optical system consisting of lenses and/or free space in a unified manner. Expressions derived using it are parametrised in terms of the parameters of the optical system, as well as those of the digital camera: aperture size, pixel size and pixel pitch. We develop rules of thumb for selecting an optical system to minimise mean squared error for given input and digital camera parameters. In the limit, our results constitute a point spread function analysis. The results presented in this paper will allow digital holography practitioners to select an optical system to maximise the quality of their reconstructed image using a priori knowledge of the camera and object