Texture features based microscopic image classification of liver cellular granuloma using artificial neural networks

Automated classification of Schistosoma mansoni granulomatous microscopic images of mice liver using Artificial Intelligence (AI) technologies is a key issue for accurate diagnosis and treatment. In this paper, three grey difference statistics-based features, namely three Gray-Level Co-occurrence Matrix (GLCM) based features and fifteen Gray Gradient Co-occurrence Matrix (GGCM) features were calculated by correlative analysis. Ten features were selected for three-level cellular granuloma classification using a Scaled Conjugate Gradient Back-Propagation Neural Network (SCG-BPNN) in the same performance. A cross-entropy is then calculated to evaluate the proposed Sigmoid input and the ten-hidden layer network. The results depicted that SCG-BPNN with texture features performs high recognition rate compared to using morphological features, such as shape, size, contour, thickness and other geometry-based features for the classification. The proposed method also has a high accuracy rate of 87.2% compared to the Back-Propagation Neural Network (BPNN), Back-Propagation Hopfield Neural Network (BPHNN) and Convolutional Neural Network (CNN)

Untersuchung von Magnetostriktiven und Piezotronischen Mikrostrukturen und Materialien für biomagnetische Sensoren mittels Röntgenstrahlen

Detecting electric potential differences from the human physiology is an established technique in medical diagnosis, e.g., as electrocardiogram. It arises from a changing electrical polarization of living cells. Simultaneously, biomagnetism is induced and can be utilized for medical examinations, as well. Benefits in using magnetic signals are, no need for direct skin contact and an increased spatial resolution, e.g., for mapping brain activity, especially in combination with electrical examinations. But biomagnetic signals are very weak and, thus, highly sensitive devices are necessary. The development of small and easy to use biomagnetic sensors, with a sufficient sensitivity, is the goal of the Collaborative Research Centre 1261 - Magnetoelectric Sensors: From Composite Materials to Biomagnetic Diagnostics. This thesis was written as part of this collaboration, with the main focus on the investigation of crystalline structures and structure related properties of piezotronic and magnetostrictive materials by utilizing a selection of X-ray techniques, i.e., X-ray diffraction (XRD), X-ray reflectivity (XRR) and coherent X-ray diffraction imaging (CXDI). Piezotronics, realized by combining piezoelectricity and Schottky contacts in one structure, provides a promising path to enhance sensor sensitivity. A first study investigated the crystalline structure of three piezotronic ZnO rods, spatially resolved by scanning nano XRD and combined with electrical examinations of their Schottky contact properties. It is found that the crystalline quality has a clear impact on the electrical properties of the related Schottky contact, probably due to crystalline defects. A complementary transmission electron microscopy (TEM) and XRD study performed on hybride vapor phase epitaxy (HVPE) grown GaN showed a slight, photoelectrochemical etching related relaxion of strain originating from crystal growth. In a separate study, CXDI was utilized for three-dimensional visualization of strain in a gold coated ZnO rod, with spatial resolution below 30 nm. A distinct strain distribution was found inside the rod, denoted to depletion and screening effects occurring in bent piezotronic structures, and a high strain at the interface may be related to Schottky contact formation. This interface strain agrees with results obtained from TEM. A succeeding CXDI study was conducted on a ZnO rod coated with magnetostrictive FeCoSiB and the possibility for the investigation of the Schottky contacts electrical properties. It was found that FeCoSiB sputtered on ZnO results in an ohmic contact and that an external magnetic field causes a change of the electrical properties, probably due to a strain change, visualized by CXDI. In a fifth study, magnetostrictive FeCo/TiN multilayer structures were investigated by a combined TEM and XRD/XRR approach, showing a relaxation of the structure due to an annealing process and a cube-on-cube structure of the FeCo and TiN layers

Light-sheet microscopy: a tutorial

This paper is intended to give a comprehensive review of light-sheet (LS) microscopy from an optics perspective. As such, emphasis is placed on the advantages that LS microscope configurations present, given the degree of freedom gained by uncoupling the excitation and detection arms. The new imaging properties are first highlighted in terms of optical parameters and how these have enabled several biomedical applications. Then, the basics are presented for understanding how a LS microscope works. This is followed by a presentation of a tutorial for LS microscope designs, each working at different resolutions and for different applications. Then, based on a numerical Fourier analysis and given the multiple possibilities for generating the LS in the microscope (using Gaussian, Bessel, and Airy beams in the linear and nonlinear regimes), a systematic comparison of their optical performance is presented. Finally, based on advances in optics and photonics, the novel optical implementations possible in a LS microscope are highlighted.Peer ReviewedPostprint (published version

Development of Microscopy Systems for Super-Resolution, Whole-Slide, Hyperspectral, and Confocal Imaging

Optical microscope is an important tool for researchers to study small objects. In this thesis, we will focus on the improvement of traditional microscope systems from several aspects including resolution, field of view, speed, cost, compactness, multimodality. In particular, we will investigate computational imaging methods that bypass the limitations with traditional microscope systems by combining the optical hardware design and image processing algorithm. Examples will include optimizing illumination strategy for the Fourier ptychography (FP), developing field-portable high-resolution microscope using a cellphone lens, investigating pattern-illuminated FP for fluorescence microscopy, demonstrating multimodal microscopic imaging with the use of liquid crystal display, achieving fast and accurate autofocusing for whole slide imaging system

Retrieving spin textures on curved magnetic thin films with full-field soft X-ray microscopies

X-ray tomography is a well-established technique to characterize 3D structures in material sciences and biology; its magnetic analogue--magnetic X-ray tomography--is yet to be developed. Here we demonstrate the visualization and reconstruction of magnetic domain structures in a 3D curved magnetic thin films with tubular shape by means of full-field soft X-ray microscopies. The 3D arrangement of the magnetization is retrieved from a set of 2D projections by analysing the evolution of the magnetic contrast with varying projection angle. Using reconstruction algorithms to analyse the angular evolution of 2D projections provides quantitative information about domain patterns and magnetic coupling phenomena between windings of azimuthally and radially magnetized tubular objects. The present approach represents a first milestone towards visualizing magnetization textures of 3D curved thin films with virtually arbitrary shape

Design, Implementation, and Evaluation of a Fluorescence Laminar Optical Tomography Scanner for Brain Imaging

Implementation of new instrumentation and techniques for neuroscience research in recent years has opened new avenues in the study of the dynamics of large-scale neural networks such as the brain. In many of these techniques, including fluorescence recordings and optogenetic stimulation, a combination of photonics and molecular genetic methods are exploited to manipulate and monitor neural activities. Such techniques have been proven to be highly efficient in unraveling the mysteries of data processing in the micro circuits of the brain and as a result these techniques are widely used nowadays in most neuroscience labs. In optogenetics, cell-types of interest are genetically modified by expressing light-sensitive proteins adapted from microbial opsin. Once these proteins are expressed, we are able to use light of appropriate wavelengths to manipulate, increase or suppress neural activity of specific neurons on command. With a high temporal resolution (in the order of milliseconds) and cell-type-specific precision, optogenetics is able to probe how the nervous system functions in real-time, even in freely-moving animals. Currently, whenever genetic modifications are employed in the study of nervous systems, fluorescence proteins are also co-expressed in the same cells as biological markers to visualize the induced changes in the targeted cells. Despite its importance to trace the signal of such markers in-vivo, capabilities of the developed fluorescence tomography instrumentation are still limited and researchers mostly document the fluorescence distribution and expression of proteins of interest after euthanizing the animal and dissection of the tissue. In this project, we present our effort in implementing a fluorescence laminar optical tomography (FLOT) system which is specifically designed for non-invasive three dimensional imaging of fluorescence proteins within the brain of rodents. The application of the developed technology is not limited to optogenetics, but it can be used as a powerful tool to help improving the precision and accuracy of neuroscience and optogenetic experiments. In this design, a set of galvanometer mirrors are employed for realization of a fast and flexible scanner while a highly sensitive camera records the produced fluorescence signals. Fluorescence laminar optical tomography (FLOT) scanner has shown promising results in imaging superficial areas up to 2mm deep from the surface, with the resolution of ~200µm. Details of the design of the hardware and reconstruction algorithms are discussed and samples of experimental results are presented

Technical implementations of light sheet microscopy

Fluorescence-based microscopy is among the most successful methods in biological studies. It played a critical role in the visualization of subcellular structures and in the analysis of complex cellular processes, and it is nowadays commonly employed in genetic and drug screenings. Among the fluorescence-based microscopy techniques, light sheet fluorescence microscopy (LSFM) has shown a quite interesting set of benefits. The technique combines the speed of epi-fluorescence acquisition with the optical sectioning capability typical of confocal microscopes. Its unique configuration allows the excitation of only a thin plane of the sample, thus fast, high resolution imaging deep inside tissues is nowadays achievable. The low peak intensity with which the sample is illuminated diminishes phototoxic effects and decreases photobleaching of fluorophores, ensuring data collection for days with minimal adverse consequences on the sample. It is no surprise that LSFM applications have raised in just few years and the technique has been applied to study a wide variety of samples, from whole organism, to tissues, to cell clusters, and single cells. As a consequence, in recent years numerous set-ups have been developed, each one optimized for the type of sample in use and the requirements of the question at hand. Hereby, we aim to review the most advanced LSFM implementations to assist new LSFM users in the choice of the LSFM set-up that suits their needs best. We also focus on new commercial microscopes and do-it-yourself strategies; likewise we review recent designs that allow a swift integration of LSFM on existing microscopes

Complex photonic structures in nature: from order to disorder

Structural colours arise from the interaction of visible light with nano-structured materials. The occurrence of such structures in nature has been known for over a century, but it is only in the last few decades that the study of natural photonic structures has fully matured due to the advances in imagining techniques and computational modelling. Even though a plethora of different colour-producing architectures in a variety of species has been investigated, a few significant questions are still open: how do these structures develop in living organisms? Does disorder play a functional role in biological photonics? If so, is it possible to say that the optical response of natural disordered photonics has been optimised under evolutionary pressure? And, finally, can we exploit the well-adapted photonic design principles that we observe in Nature to fabricate functional materials with optimised scattering response? In my thesis I try to answer the questions above: I microscopically investigate $\textit{in vivo}$ the growth of a cuticular multilayer, one of the most common colour-producing strategies in nature, in the green beetles $\textit{Gastrophysa viridula}$ showing how the interplay between different materials varies during the various life stages of the beetles; I further investigate two types of disordered photonic structures and their biological role, the random array of spherical air inclusions in the eggshells of the honeyguide $\textit{Prodotiscus regulus}$, a species under unique evolutionary pressure to produce blue eggs, and the anisotropic chitinous network of fibres in the white beetle $\textit{Cyphochilus}$, the whitest low-refractive index material; finally, inspired by these natural designs, I fabricate and study light transport in biocompatible highly-scattering materials.European Research Council grant awarded to Dr Silvia Vignolin