Crop row detection in maize fields inspired on the human visual perception

This paper proposes a new method, oriented to image real-time processing, for identifying crop rows in maize fields in the images. The vision system is designed to be installed onboard a mobile agricultural vehicle, that is, submitted to gyros, vibrations, and undesired movements. The images are captured under image perspective, being affected by the above undesired effects. The image processing consists of two main processes: image segmentation and crop row detection. The first one applies a threshold to separate green plants or pixels (crops and weeds) from the rest (soil, stones, and others). It is based on a fuzzy clustering process, which allows obtaining the threshold to be applied during the normal operation process. The crop row detection applies a method based on image perspective projection that searches for maximum accumulation of segmented green pixels along straight alignments. They determine the expected crop lines in the images. The method is robust enough to work under the above-mentioned undesired effects. It is favorably compared against the well-tested Hough transformation for line detection.

Diseño de la sala 6 de Kinépolis (Madrid) con un sistema Dolby ATMOS

El objetivo de este Proyecto Fin de Carrera es el estudio y simulación de la sonorización de una sala de cine mediante la utilización del sistema DOLBY ATMOS. Para ello, se simulará la sala 6 del complejo de cines Kinépolis de Madrid utilizando el programa de simulación electroacústica EASE en el que se dispondrá el sistema de sonido DOLBY ATMOS. Primero se procederá a realizar el modelo geométrico en el programa EASE, a partir de los planos de la instalación y medidas realizadas en el recinto. Este programa de simulación permite obtener los parámetros acústicos y electroacústicos necesarios para realizar el estudio de la sala. Luego se diseñará el sistema de sonido de acuerdo a las disposiciones del sistema DOLBY ATMOS, mediante la ubicación de sistemas de altavoces de cine existentes en el mercado, siempre intentando mantener el uso de la sala de forma convencional como DOLBY DIGITAL y cumpliendo los requisitos de uniformidad y ángulos de apuntamiento recomendados por DOLBY. A continuación, una vez dispuestos los altavoces, se procederá a su configuración, realizando una ecualización y ajuste de nivel de manera individual para cada una de las fuentes sonoras, tanto de los altavoces de pantalla, altavoces de surround de pared y techo y los altavoces de subgraves. Como resultado de todo ello, se comprobarán parámetros como la inteligibilidad, respuesta impulsiva, respuesta en frecuencia y tiempo de reverberación en diferentes puntos de escucha, comparando los resultados obtenidos entre ellos. También se realizará una configuración compatible con el sistema de sonido 7.1, realizando su correspondiente configuración, ecualización, ajuste y aplicando los retardos necesarios. Una vez esté todo configurado, será dar un presupuesto de lo que supondría la reformar de un cine convencional a un sistema DOLBY ATMOS, teniendo en cuenta el número de altavoces disponibles en la sala actual, los modelos utilizados, amplificadores y mano de obra. También se realizará un diagrama de conexionado del sistema de sonido utilizado en el proyecto, incluyendo todos los parámetros necesarios de la configuración. Por último se comprobará la viabilidad técnica y económica del sistema diseñado, viendo cuál es la opción que más se adecua a cada necesidad y sugiriendo soluciones a los posibles problemas que se puedan encontrar. ABSTRACT. The main aim of this Project is the study and simulation of the sound of a movie theater by using DOLBY ATMOS system. It is going to be simulated the movie theatre 6 at Kinepolis cinema complex in Madrid using the simulation program EASE according to the sound system DOLBY ATMOS. First of all we proceed to conduct the geometric pattern in the EASE program, from installation drawings and measurements made on the premises. This simulation program allows getting the acoustic and electroacoustic parameters necessary for the study of the theatre. Then the sound system designed according to the suggestions of ATMOS DOLBY, by locating theater speaker systems on the market, always trying to keep the use of the room for DOLBY DIGITAL conventional and meeting the requirements of uniformity and pointing angles DOLBY recommended. Then, once the speakers are prepared, you can proceed to configure, make equalization and level setting individually for each of the sound sources, both screen speakers, surround speakers (wall and ceiling) and subwoofer. As a result, parameters are checked as intelligibility, impulse response, frequency response and reverberation time in different listening points, comparing the results between each other. There will also be configured to support 7.1 sound system, making the corresponding settings, equalization, level setting and applying the necessary delays. Once everything is configured, it will give an estimate of what would be the reform of a conventional film DOLBY ATMOS system, taking into account the number of speakers available in the current room, the models used, amplifiers and labor. Also there will be a wiring diagram of the sound system used in this project, including all of the configuration parameters needed. Finally, check the technical and economic feasibility of the designed system, seeing what is the option that best suits to each need and suggesting possible solutions to problems you might find during the process.

Optimización de una energía mediante cortes de grafos. Segmentación de imágenes

La segmentación de imágenes puede plantearse como un problema de minimización de una energía discreta. Nos enfrentamos así a una doble cuestión: definir una energía cuyo mínimo proporcione la segmentación buscada y, una vez definida la energía, encontrar un mínimo absoluto de la misma. La primera parte de esta tesis aborda el segundo problema, y la segunda parte, en un contexto más aplicado, el primero. Las técnicas de minimización basadas en cortes de grafos permiten obtener el mínimo de una energía discreta en tiempo polinomial mediante algoritmos de tipo min-cut/max-flow. Sin embargo, estas técnicas solo pueden aplicarse a energías que son representabas por grafos. Un importante reto es estudiar qué energías son representabas así como encontrar un grafo que las represente, lo que equivale a encontrar una función gadget con variables adicionales. En la primera parte de este trabajo se estudian propiedades de las funciones gadgets que permiten acotar superiormente el número de variables adicionales. Además se caracterizan las energías con cuatro variables que son representabas, definiendo gadgets con dos variables adicionales. En la segunda parte, más práctica, se aborda el problema de segmentación de imágenes médicas, base en muchas ocasiones para la diagnosis y el seguimiento de terapias. La segmentación multi-atlas es una potente técnica de segmentación automática de imágenes médicas, con tres aspectos importantes a destacar: el tipo de registro entre los atlas y la imagen objetivo, la selección de atlas y el método de fusión de etiquetas. Este último punto puede formularse como un problema de minimización de una energía. A este respecto introducimos dos nuevas energías representables. La primera, de orden dos, se utiliza en la segmentación en hígado y fondo de imágenes abdominales obtenidas mediante tomografía axial computarizada. La segunda, de orden superior, se utiliza en la segmentación en hipocampos y fondo de imágenes cerebrales obtenidas mediante resonancia magnética. ABSTRACT The image segmentation can be described as the problem of minimizing a discrete energy. We face two problems: first, to define an energy whose minimum provides the desired segmentation and, second, once the energy is defined we must find its global minimum. The first part of this thesis addresses the second problem, and the second part, in a more applied context, the first problem. Minimization techniques based on graph cuts find the minimum of a discrete energy in polynomial time via min-cut/max-flow algorithms. Nevertheless, these techniques can only be applied to graph-representable energies. An important challenge is to study which energies are graph-representable and to construct graphs which represent these energies. This is the same as finding a gadget function with additional variables. In the first part there are studied the properties of gadget functions which allow the number of additional variables to be bounded from above. Moreover, the graph-representable energies with four variables are characterised and gadgets with two additional variables are defined for these. The second part addresses the application of these ideas to medical image segmentation. This is often the first step in computer-assisted diagnosis and monitoring therapy. Multiatlas segmentation is a powerful automatic segmentation technique for medical images, with three important aspects that are highlighted here: the registration between the atlas and the target image, the atlas selection, and the label fusion method. We formulate the label fusion method as a minimization problem and we introduce two new graph-representable energies. The first is a second order energy and it is used for the segmentation of the liver in computed tomography (CT) images. The second energy is a higher order energy and it is used for the segmentation of the hippocampus in magnetic resonance images (MRI).

Three-dimensional mapping of real environments for cognitive robots navigation

Abstract The development of cognitive robots needs a strong “sensorial” support which should allow it to perceive the real world for interacting with it properly. Therefore the development of efficient visual-processing software to be equipped in effective artificial agents is a must. In this project we study and develop a visual-processing software that will work as the “eyes” of a cognitive robot. This software performs a three-dimensional mapping of the robot’s environment, providing it with the essential information required to make proper decisions during its navigation. Due to the complexity of this objective we have adopted the Scrum methodology in order to achieve an agile development process, which has allowed us to correct and improve in a fast way the successive versions of the product. The present project is structured in Sprints, which cover the different stages of the software development based on the requirements imposed by the robot and its real necessities. We have initially explored different commercial devices oriented to the acquisition of the required visual information, adopting the Kinect Sensor camera (Microsoft) as the most suitable option. Later on, we have studied the available software to manage the obtained visual information as well as its integration with the robot’s software, choosing the high-level platform Matlab as the common nexus to join the management of the camera, the management of the robot and the implementation of the behavioral algorithms. During the last stages the software has been developed to include the fundamental functionalities required to process the real environment, such as depth representation, segmentation, and clustering. Finally the software has been optimized to exhibit real-time processing and a suitable performance to fulfill the robot’s requirements during its operation in real situations.

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

The structural connectivity of the brain is considered to encode species-wise and subject-wise patterns that will unlock large areas of understanding of the human brain. Currently, diffusion MRI of the living brain enables to map the microstructure of tissue, allowing to track the pathways of fiber bundles connecting the cortical regions across the brain. These bundles are summarized in a network representation called connectome that is analyzed using graph theory. The extraction of the connectome from diffusion MRI requires a large processing flow including image enhancement, reconstruction, segmentation, registration, diffusion tracking, etc. Although a concerted effort has been devoted to the definition of standard pipelines for the connectome extraction, it is still crucial to define quality assessment protocols of these workflows. The definition of quality control protocols is hindered by the complexity of the pipelines under test and the absolute lack of gold-standards for diffusion MRI data. Here we characterize the impact on structural connectivity workflows of the geometrical deformation typically shown by diffusion MRI data due to the inhomogeneity of magnetic susceptibility across the imaged object. We propose an evaluation framework to compare the existing methodologies to correct for these artifacts including whole-brain realistic phantoms. Additionally, we design and implement an image segmentation and registration method to avoid performing the correction task and to enable processing in the native space of diffusion data. We release PySDCev, an evaluation framework for the quality control of connectivity pipelines, specialized in the study of susceptibility-derived distortions. In this context, we propose Diffantom, a whole-brain phantom that provides a solution to the lack of gold-standard data. The three correction methodologies under comparison performed reasonably, and it is difficult to determine which method is more advisable. We demonstrate that susceptibility-derived correction is necessary to increase the sensitivity of connectivity pipelines, at the cost of specificity. Finally, with the registration and segmentation tool called regseg we demonstrate how the problem of susceptibility-derived distortion can be overcome allowing data to be used in their original coordinates. This is crucial to increase the sensitivity of the whole pipeline without any loss in specificity.

Modelo para la medición con máquinas de visión e iluminación episcópica mediante la aplicación de técnicas de resolución subpíxel y aproximación bayesiana

En esta tesis se desarrolla un modelo físico-matemático, original, que permite simular el comportamiento de las máquinas de visión, en particular las máquinas ópticas digitales, cuando reciben información a través de la luz reflejada por los mensurandos. El modelo desarrollado se lia aplicado para la determinación de los parámetros que intervienen en el proceso de caracterización de formas geométricas básicas, tales como líneas, círculos y elipses. También se analizan las fuentes de error que intervienen a lo largo de la cadena metrológica y se proponen modelos de estimación de las incertidumbres de medida a través un nuevo enfoque basado en estadística bayesiana y resolución subpíxel. La validez del modelo se ha comprobado por comparación de los resultados teóricos, obtenidos a partir de modelos virtuales y simulaciones informáticas, y los reales, obtenidos mediante la realización de medidas de diferentes mensurandos del ámbito electromecánico y de dimensiones submilimétricas. Utilizando el modelo propuesto, es posible caracterizar adecuadamente mensurandos a partir del filtrado, segmentación y tratamiento matemático de las imágenes. El estudio experimental y validación definitiva de los resultados se ha realizado en el Laboratorio de Metrología Dimensional de la Escuela Técnica Superior de Ingeniería y Diseño Industrial de la Universidad Politécnica de Madrid. Los modelos desarrollados se han implementado sobre imágenes obtenidas con la máquina de visión marca TESA, modelo VISIO 300. Abstract In this PhD Thesis an original mathematic-physic model has been developed. It allows simulating the behaviour of the vision measuring machines, in particular the optical digital machines, where they receive information through the light reflected by the measurands. The developed model has been applied to determine the parameters involved in the process of characterization of basic geometrical features such as lines, circles and ellipses. The error sources involved along the metrological chain also are analyzed and new models for estimating measurement uncertainties through a new approach based on Bayesian statistics and subpixel resolution are proposed. The validity of the model has been verified by comparing the theoretical results obtained from virtual models and computer simulations, with actual ones, obtained by measuring of various measurands belonging to the electromechanical field and of submillimeter dimensions. Using the proposed model, it is possible to properly characterize measurands from filtering, segmentation and mathematical processing of images. The experimental study and final validation of the results has been carried out in the "Laboratorio de Metrología Dimensional" (Dimensional Metrology Laboratory) at the Escuela Técnica Superior de Ingeniería y Diseño Industrial (ETSIDI) (School of Engineering and Industrial Design) at Universidad Politécnica de Madrid (UPM). The developed models have been implemented on images obtained with the vision measuring machine of the brand TESA, model VISIO 300.

Evolution of the bilaterian body plan: What have we learned from annelids?

Annelids, unlike their vertebrate or fruit fly cousins, are a bilaterian taxon often overlooked when addressing the question of body plan evolution. However, recent data suggest that annelids offer unique insights on the early evolution of spiral cleavage, anteroposterior axis formation, body axis segmentation, and head versus trunk distinction.

A JAK-STAT pathway regulates wing vein formation in Drosophila.

We present evidence that the JAK-STAT signal transduction pathway regulates multiple developmental processes in Drosophila. We screened for second-site mutations that suppress the phenotype of the hyperactive hopTum-1 Jak kinase, and recovered a mutation that meiotically maps to the known chromosomal position of D-Stat, a Drosophila stat gene. This hypomorphic mutation, termed statHJ contains a nucleotide substitution in the first D-Stat intron, resulting in a reduction in the number of correctly processed transcripts. Further, the abnormally processed mRNA encodes a truncated protein that has a dominant negative effect on transcriptional activation by the wild-type cDNA in cell culture. statHJ mutants exhibit patterning defects that include the formation of ectopic wing veins, similar to those seen in mutants of the epidermal growth factor/receptor pathway. Abnormalities in embryonic and adult segmentation and in tracheal development were also observed. The hopTum-1 and statHJ mutations can partially compensate for each other genetically, and Hop overexpression can increase D-Stat transcriptional activity in vitro, indicating that the gene products interact in a common regulatory pathway.

Cortical activity flips among quasi-stationary states.

Parallel recordings of spike trains of several single cortical neurons in behaving monkeys were analyzed as a hidden Markov process. The parallel spike trains were considered as a multivariate Poisson process whose vector firing rates change with time. As a consequence of this approach, the complete recording can be segmented into a sequence of a few statistically discriminated hidden states, whose dynamics are modeled as a first-order Markov chain. The biological validity and benefits of this approach were examined in several independent ways: (i) the statistical consistency of the segmentation and its correspondence to the behavior of the animals; (ii) direct measurement of the collective flips of activity, obtained by the model; and (iii) the relation between the segmentation and the pair-wise short-term cross-correlations between the recorded spike trains. Comparison with surrogate data was also carried out for each of the above examinations to assure their significance. Our results indicated the existence of well-separated states of activity, within which the firing rates were approximately stationary. With our present data we could reliably discriminate six to eight such states. The transitions between states were fast and were associated with concomitant changes of firing rates of several neurons. Different behavioral modes and stimuli were consistently reflected by different states of neural activity. Moreover, the pair-wise correlations between neurons varied considerably between the different states, supporting the hypothesis that these distinct states were brought about by the cooperative action of many neurons.

Classifying image analysis techniques from their output

In this paper we discuss some main image processing techniques in order to propose a classification based upon the output these methods provide. Because despite a particular image analysis technique can be supervised or unsupervised, and can allow or not the existence of fuzzy information at some stage, each technique has been usually designed to focus on a specific objective, and their outputs are in fact different according to each objective. Thus, they are in fact different methods. But due to the essential relationship between them they are quite often confused. In particular, this paper pursues a clarification of the differences between image segmentation and edge detection, among other image processing techniques.

Analysis of fixational eye micromovements through pupil tracking

Póster presentado en OPTYKA Optical Fair 2012, Poznan, Polonia, 9-10 noviembre 2012.

MRI Registration for Human Hip Kinematics

Measurement of joint kinematics can provide knowledge to help improve joint prosthesis design, as well as identify joint motion patterns that may lead to joint degeneration or injury. More investigation into how the hip translates in live human subjects during high amplitude motions is needed. This work presents a design of a non-invasive method using the registration between images from conventional Magnetic Resonance Imaging (MRI) and open MRI to calculate three dimensional hip joint kinematics. The method was tested on a single healthy subject in three different poses. MRI protocols for the conventional gantry, high-resolution MRI and the open gantry, lowresolution MRI were developed. The scan time for the low-resolution protocol was just under 6 minutes. High-resolution meshes and low resolution contours were derived from segmentation of the high-resolution and low-resolution images, respectively. Low-resolution contours described the poses as scanned, whereas the meshes described the bones’ geometries. The meshes and contours were registered to each other, and joint kinematics were calculated. The segmentation and registration were performed for both cortical and sub-cortical bone surfaces. A repeatability study was performed by comparing the kinematic results derived from three users’ segmentations of the sub-cortical bone surfaces from a low-resolution scan. The root mean squared error of all registrations was below 1.92mm. The maximum range between segmenters in translation magnitude was 0.95mm, and the maximum deviation from the average of all orientations was 1.27◦. This work demonstrated that this method for non-invasive measurement of hip kinematics is promising for measuring high-range-of-motion hip motions in vivo.

Revisiting the involvement of signaling gradients in somitogenesis

During embryonic development, formation of individual vertebrae requires that the paraxial mesoderm becomes divided into regular segmental units known as somites. Somites are sequentially formed at the anterior end of the presomitic mesoderm (PSM) resulting from functional interactions between the oscillatory activity of signals promoting segmentation and a moving wavefront of tissue competence to those signals, eventually generating a constant flow of new somites at regular intervals. According to the current model for somitogenesis, the wavefront results from the combined activity of two opposing functional gradients in the PSM involving the Fgf, Wnt and retinoic acid (RA) signaling pathways. Here, I use published data to evaluate the wavefront model. A critical analysis of those studies seems to support a role for Wnt signaling, but raise doubts regarding the extent to which Fgf and RA signaling contribute to this process.

Physical models of dilatant normal faulting in jointed cohesive rocks

Dilatant faults often form in rocks containing pre-existing joints, but the effects of joints on fault segment linkage and fracture connectivity is not well understood. We present an analogue modeling study using cohesive powder with pre-formed joint sets in the upper layer, varying the angle between joints and a rigid basement fault. We analyze interpreted map-view photographs at maximum displacement for damage zone width, number of connected joints, number of secondary fractures, degree of segmentation and area fraction of massively dilatant fractures. Particle imaging velocimetry helps provide insights on deformation history of the experiments and illustrate the localization pattern of fault segments. Results show that with increasing angle between joint-set and basement-fault strike the number of secondary fractures and the number of connected joints increases, while the area fraction of massively dilatant fractures shows only a minor increase. Models without pre-existing joints show far lower area fractions of massively dilatant fractures while forming distinctly more secondary fractures.

Segmenting eukaryotic genomes with the generalized Gibbs sampler

Eukaryotic genomes display segmental patterns of variation in various properties, including GC content and degree of evolutionary conservation. DNA segmentation algorithms are aimed at identifying statistically significant boundaries between such segments. Such algorithms may provide a means of discovering new classes of functional elements in eukaryotic genomes. This paper presents a model and an algorithm for Bayesian DNA segmentation and considers the feasibility of using it to segment whole eukaryotic genomes. The algorithm is tested on a range of simulated and real DNA sequences, and the following conclusions are drawn. Firstly, the algorithm correctly identifies non-segmented sequence, and can thus be used to reject the null hypothesis of uniformity in the property of interest. Secondly, estimates of the number and locations of change-points produced by the algorithm are robust to variations in algorithm parameters and initial starting conditions and correspond to real features in the data. Thirdly, the algorithm is successfully used to segment human chromosome 1 according to GC content, thus demonstrating the feasibility of Bayesian segmentation of eukaryotic genomes. The software described in this paper is available from the author's website (www.uq.edu.au/similar to uqjkeith/) or upon request to the author.