MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

http://ieeexplore.ieee.org/iel2/4524/12820/00592460.pdf

Image Processing

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner ‘nutritious seeds for a sustainable future’. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.

/pdf/neglecting-legumes-has-compromised-human-health-and-2vzbf3diuf.pdf

Neglecting legumes has compromised human health and sustainable food production

Breeding for resistance to biotic and abiotic stresses of global importance in common bean is reviewed with emphasis on development and application of marker-assisted selection (MAS). The implementation and adoption of MAS in breeding for disease resistance is advanced compared to the implementation of MAS for insect and abiotic stress resistance. Highlighted examples of breeding in common bean using molecular markers reveal the role and success of MAS in gene pyramiding, rapidly deploying resistance genes via marker-assisted backcrossing, enabling simpler detection and selection of resistance genes in absence of the pathogen, and contributing to simplified breeding of complex traits by detection and indirect selection of quantitative trait loci (QTL) with major effects. The current status of MAS in breeding for resistance to angular leaf spot, anthracnose, Bean common mosaic and Bean common mosaic necrosis viruses, Beet curly top virus, Bean golden yellow mosaic virus, common bacterial blight, halo bacterial blight, rust, root rots, and white mold is reviewed in detail. Cumulative mapping of disease resistance traits has revealed new resistance gene clusters while adding to others, and reinforces the co-location of QTL conditioning resistance with specific resistance genes and defense-related genes. Breeding for resistance to insect pests is updated for bean pod weevil (Apion), bruchid seed weevils, leafhopper, thrips, bean fly, and whitefly, including the use of arcelin proteins as selectable markers for resistance to bruchid seed weevils. Breeding for resistance to abiotic stresses concentrates on drought, low soil phosphorus, and improved symbiotic nitrogen fixation. The combination of root growth and morphology traits, phosphorus uptake mechanisms, root acid exudation, and other traits in alleviating phosphorus deficiency, and identification of numerous QTL of relatively minor effect associated with each trait, reveals the complexity to be addressed in breeding for abiotic stress resistance in common bean.

Common bean breeding for resistance against biotic and abiotic stresses: From classical to MAS breeding

Adaptive optics is becoming a valuable tool for high resolution microscopy, providing correction for aberrations introduced by the refractive index structure of specimens. This is proving particularly promising for applications that require images from deep within biological tissue specimens. We review recent developments in adaptive microscopy, including methods and applications. A range of advances in different microscope modalities is covered and prospects for the future are discussed. Adaptive optics is used to improve image quality across a wide range of microscopy techniques. Martin Booth from the University of Oxford in the UK reviews how technologies such as deformable mirrors and spatial light modulators, which compensate for aberrations by locally controlling the wavefront of a light wave, are now improving the performance of multiphoton, confocal, widefield and super-resolution microscopes. The benefits of such improvements are especially appealing for images captured from within biological tissue (focal distances of tens to hundreds of micrometres), where low-order aberrations associated with smooth phase variations occur. One future challenge is the development of efficient measurement and correction schemes for higher-order phase variations.

Adaptive optical microscopy: the ongoing quest for a perfect image

Corneal structure and transparency

Genetic improvement of common beans and the challenges of climate change.

A Mueller-matrix polarimeter in transmission mode using two electronically controlled liquid-crystal variable retarders has been developed. Its design, theory and calibration are described. Although liquid crystals have been proposed earlier, this paper is focused on the process of the calculation of the Mueller matrix by a matrix-inversion method, oriented to static systems and in vitro samples. By driving the retarders with appropriate voltages, nine independent pairs of polarization states can be produced (incomplete polarimetry), while the other additional seven pairs are obtained by placing two quarter-wave plates (in the input and output optical paths respectively). This configuration allows extraction of 16 independent measurements of intensity. The Mueller matrix of the sample is calculated from them. The results of Mueller matrices for air, a linear polarizer and a quarter-wave plate are presented. Additional polarization parameters such as retardation, ellipticity or degree of polarization were also computed and some applications of the system are proposed.

https://iopscience.iop.org/article/10.1088/1464-4258/2/3/308/pdf

Polarimetry using liquid-crystal variable retarders : theory and calibration

PURPOSE. To describe monochromatic optical aberrations of the eye as a function of age. METHODS. One hundred fourteen subjects with a spherical equivalent within 3.50 D from emmetropia, corrected visual acuity of 20/40 or better, and normal findings in an ophthalmic examination were enrolled. The mean age was 43.2 24.5 years (range, 5.7‐ 82.3). Monochromatic optical aberrations were measured with a Hartmann-Shack wavefront sensor after pharmacological dilation and cycloplegia. RESULTS. For a 5-mm pupil and for third- to seventh-, third-, fourth-, and fifth- to seventh-order aberrations, as well as for coma and spherical aberrations, the root mean square (RMS) error as a function of age was modeled by a second-order polynomial regression. It decreased progressively through childhood, adolescence, and early adulthood; reached a minimum level during the fourth decade of life, then increased progressively with age, to age 82. For a 5-mm pupil, the mean modulation transfer function (MTF) was reduced in both the child- teenage (5‐20 years; n 29) and the elderly (61‐ 82 years; n 37) groups versus the middle-aged adult group (41‐ 60 years; n 24; P 0.05). In young adults (21‐ 40 years; n 23) and elderly subjects, the MTF curves were very close and almost superimposed at spatial frequencies higher than 38 cyc/deg. CONCLUSIONS. Aberrations of the whole eye were objectively measured from early childhood to an advanced age, and the relationship between monochromatic aberrations and age has been shown to fit a quadratic model. The results suggest that the definition of emmetropization should be broadened to include the reduction of higher order aberrations. (Invest Ophthalmol Vis Sci. 2003;44:5438‐5446) DOI:10.1167/iovs.02-1042

Monochromatic aberrations as a function of age, from childhood to advanced age.

A Mueller-matrix imaging polarimeter was developed to measure spatially resolved polarization properties in the living human eye The apparatus is a double-pass setup that incorporates two liquid-crystal variable retarders and a slow-scan CCD camera in the recording stage Series of 16 images for the combinations of independent polarization states in the first and second passages were recorded for two experimental conditions:?with the camera conjugated either with the retina or with the eye's pupil plane Spatially resolved collections of Mueller matrices and the degree of polarization were calculated from those images for both retinal and pupil planes

Juan M. Bueno

Papers

Genetic improvement of common beans and the challenges of climate change.

Polarimetry using liquid-crystal variable retarders : theory and calibration

Monochromatic aberrations as a function of age, from childhood to advanced age.

Double-pass imaging polarimetry in the human eye.

Spatially resolved polarization properties for in vitro corneas.