3D SEM Surface Reconstruction: An Optimized, Adaptive, and Intelligent Approach

Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, including biological, mechanical, and material sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and information about their three-dimensional (3D) surface structures. Having 3D surfaces from SEM images would provide true anatomic shapes of micro samples which would allow for quantitative measurements and informative visualization of the systems being investigated. In this research project, we novel design and develop an optimized, adaptive, and intelligent multi-view approach named 3DSEM++ for 3D surface reconstruction of SEM images, making a 3D SEM dataset publicly and freely available to the research community. The work is expected to stimulate more interest and draw attention from the computer vision and multimedia communities to the fast-growing SEM application area

Shape-induced force fields in optical trapping

Advances in optical tweezers, coupled with the proliferation of two-photon polymerization systems, mean that it is now becoming routine to fabricate and trap non-spherical particles. The shaping of both light beams and particles allows fine control over the flow of momentum from the optical to mechanical regimes. However, understanding and predicting the behaviour of such systems is highly complex in comparison with the traditional optically trapped microsphere. In this Article, we present a conceptually new and simple approach based on the nature of the optical force density. We illustrate the method through the design and fabrication of a shaped particle capable of acting as a passive force clamp, and we demonstrate its use as an optically trapped probe for imaging surface topography. Further applications of the design rules highlighted here may lead to new sensors for probing biomolecule mechanics, as well as to the development of optically actuated micromachines

Visualization and Analysis Techniques for Three Dimensional Information Acquired by Confocal Microscopy

Confocal Scanning Laser Microscopy (CSLM) is particularly well suited for the acquisition of 3-dimensional data of microscopic objects. In the CSLM a specific volume in the object is sampled during the imaging process and the result is stored in a digital computer as a three-dimensional memory array. Optimal use of these data requires both the development of effective visual representations as well as analysis methods. In addition to the well known stereoscopic representation method a number of alternatives for various purposes are presented. When rendering in terms of solid-looking or semitransparent objects is required, an algorithm based on a simulated process of excitation and fluorescence is very suitable. Graphic techniques can be used to examine the 3-dimensional shape of surfaces. For (near-)real time applications a representation method should not require extensive previous data-processing or analysis. From the very extensive field of 3-D image analysis two examples are given

NMR Imaging of the honeybee brain

NMR microscopy provides non-invasively distinct soft-tissue contrast in small biological samples. We were able to visualize the three-dimensional structure of the honeybee brain in its natural shape in the intact head capsule. Thus, in addition to acquiring detailed information about the shapes and volumes of the different brain compartments, we were able to show their relative orientations toward each other within the head capsule. Since the brain was lightly fixed but not dehydrated, and stayed attached to the head capsule and its internal structures, the NMR experiments exhibited larger volumes and a more natural stereo geometry of the various brain structures compared to confocal laser microscopy experiments on dissected, dehydrated and cleared brains. Abbreviation: / CLM: confocal laser microscopy NMR: nuclear magnetic resonanc

Application of ultraviolet, visible, and infrared light imaging in protein-based biopharmaceutical formulation characterization and development studies

Imaging is increasingly more utilized as analytical technology in biopharmaceutical formulation research, with applications ranging from subvisible particle characterization to thermal stability screening and residual moisture analysis. This review offers a comprehensive overview of analytical imaging for scientists active in biopharmaceutical formulation research and development, where it presents the unique information provided by the ultraviolet (UV), visible (Vis), and infrared (IR) sections in the electromagnetic spectrum. The main body of this review consists of an outline of UV, Vis, and IR imaging techniques for several (bio)physical properties that are commonly determined during protein-based biopharmaceutical formulation characterization and development studies. The review concludes with a future perspective of applied imaging within the field of biopharmaceutical formulation research

Efficient and Accurate Disparity Estimation from MLA-Based Plenoptic Cameras

This manuscript focuses on the processing images from microlens-array based plenoptic cameras. These cameras enable the capturing of the light field in a single shot, recording a greater amount of information with respect to conventional cameras, allowing to develop a whole new set of applications. However, the enhanced information introduces additional challenges and results in higher computational effort. For one, the image is composed of thousand of micro-lens images, making it an unusual case for standard image processing algorithms. Secondly, the disparity information has to be estimated from those micro-images to create a conventional image and a three-dimensional representation. Therefore, the work in thesis is devoted to analyse and propose methodologies to deal with plenoptic images. A full framework for plenoptic cameras has been built, including the contributions described in this thesis. A blur-aware calibration method to model a plenoptic camera, an optimization method to accurately select the best microlenses combination, an overview of the different types of plenoptic cameras and their representation. Datasets consisting of both real and synthetic images have been used to create a benchmark for different disparity estimation algorithm and to inspect the behaviour of disparity under different compression rates. A robust depth estimation approach has been developed for light field microscopy and image of biological samples

The link between true larvae and parasitic forms within Isopoda – insights from the fossil record

Isopoda is a species-rich ingroup of Eucrustacea (crustaceans and insects), whose representatives live in a variety of habitats from the deep sea to arid terrestrial landscapes. Isopoda is very diverse regarding the life styles which are present in its species. There are herbivorous and detritivorous species as well as predators and scavengers. Parasitism, as an interaction between animals where one animal exploits resources from the other to it’s disadvantage, is far from being a fringe phenomenon inside Isopoda – a large proportion of species in Isopoda are either parasites or micro-predators (also referred to as temporary parasites). Parasitic forms (in the wider sense, including micro-predators) of Isopoda can be found in a few ingroups, which are generally thought to be closely related or to form a monophyletic group. Among the parasitic forms there are many species whose development includes a strong ecological and morphological differentiation between the immatures and the adults (larval development). Despite the ecological importance in modern ecosystems, the fossil record of parasitic forms of Isopoda is rather sparse. The aim of this study was to recognise and thoroughly document potentially parasitic forms of Isopoda in the fossil record, using modern imaging techniques. By interpreting the systematic positions of the extinct species, the fossil forms could be compared with closely related extant forms for which there are observations of their behaviour in their natural environment. The goal was also to recognise potentially immature forms, which could provide insights into the evolution of developmental patterns within Isopoda, especially with respect to the parasitic forms in which there seems to be a stronger tendency for differentiation between adults and their offspring. Fossils have the potential to yield combinations of characters that are not present in extant species and are thereby important to reconstruct the evolution of characters. Fossils of such value were explicitly searched for. Furthermore, the fossils inspected in the studies of this dissertation should be used to provide a temporal context to the evolution of parasitism and larval development within Isopoda. Two well-preserved fossils of presumably non-parasitic forms within the group Cymothoida (in which there are also parasitic forms) from fossilised mid-Cretaceous resin were studied (study I). One of them was interpreted as an immature, which resembles the other, larger, specimen, which is assumed to be of a later developmental stage, in most aspects of the body morphology – except for the absence of a well developed leg on the posterior-most walking leg, which absence in immatures is an apomorphy of the group Mancoidea, which comprises Isopoda. This represents, together with a recently published fossil of the same site, the oldest record of an immature specimen in Isopoda. Multiple minute fossils of the group Epicaridea (parasites of crustaceans) from two different mid- and Late Cretaceous amber localities (studies I and III) were studied. They represent the oldest body fossils of the group Epicaridea, which has a rich record of fossil traces which its representatives left on their host (growth responses by the host) while feeding on them. Based on the available morphological features, the fossils were identified as either larvae (of the cryptoniscium stage) or paedomorphic adult males. Their presence in the fossil record suggests that the complex life cycle that is found in extant species of Epicaridea was already present in the Cretaceous. An assemblage of multiple strongly compressed fossils from the Eocene of the Czech Republic was documented (study IV). The specimens were identified as being either close relatives to or representatives of group Cymothoidae (mostly parasites of fishes in the extant fauna). This marks the first and therefore oldest reliable record of this lineage in the fossil record. The assemblage contains specimens of different body sizes. Together with differences in the overall body shape this indicates the presence of immature stages. Fossils of Urda, an extinct, potentially non-monophyletic group with a unique combination of characters, were analysed (study V). The fossils are interpreted as the closest so far known relatives of the extant group Gnathiidae (temporary parasites of fishes), with which representatives they share a number of apomorphic characters; a convincing apomorphy for Urda could not be found. The fossils, for which there is no indication that they represent remains of immatures, are very similar in many aspects to immature forms of Gnathiidae, in contrast to which they, however, lack the paedomorphic absence of legs on one segment of the trunk. The occurrence of some fossils of Urda on fossils of fishes suggests a syn-vivo interaction, such as parasitism or commensalism. Fossils of Urda provide important information about the character evolution towards modern, fish-parasites of the group Gnathiidae. The evolution of larvae within Isopoda seems to be deeply interlinked with the evolution of parasitism. The fossil record yields specimens with a larval development that date back to the mid-Cretaceous. These specimens simultaneously represent the oldest fossils which can be identified as belonging to extant groups in which all species have a parasitic life style. Close relatives of extant parasites date back even further, to the Lower Jurassic. Overall, despite still being patchy, the fossil record of Isopoda provides unique insights into the evolution of parasitic forms as well as into the differentiation between adults and immature forms

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Measurement, modelling, and closed-loop control of crystal shape distribution: Literature review and future perspectives

Crystal morphology is known to be of great importance to the end-use properties of crystal products, and to affect down-stream processing such as filtration and drying. However, it has been previously regarded as too challenging to achieve automatic closed-loop control. Previous work has focused on controlling the crystal size distribution, where the size of a crystal is often defined as the diameter of a sphere that has the same volume as the crystal. This paper reviews the new advances in morphological population balance models for modelling and simulating the crystal shape distribution (CShD), measuring and estimating crystal facet growth kinetics, and two- and three-dimensional imaging for on-line characterisation of the crystal morphology and CShD. A framework is presented that integrates the various components to achieve the ultimate objective of model-based closed-loop control of the CShD. The knowledge gaps and challenges that require further research are also identified