A comprehensive review of 3D convolutional neural network-based classification techniques of diseased and defective crops using non-UAV-based hyperspectral images

Hyperspectral imaging (HSI) is a non-destructive and contactless technology that provides valuable information about the structure and composition of an object. It has the ability to capture detailed information about the chemical and physical properties of agricultural crops. Due to its wide spectral range, compared with multispectral-or RGB-based imaging methods, HSI can be a more effective tool for monitoring crop health and productivity. With the advent of this imaging tool in agrotechnology, researchers can more accurately address issues related to the detection of diseased and defective crops in the agriculture industry. This allows to implement the most suitable and accurate farming solutions, such as irrigation and fertilization, before crops enter a damaged and difficult-to-recover phase of growth in the field. While HSI provides valuable insights into the object under investigation, the limited number of HSI datasets for crop evaluation presently poses a bottleneck. Dealing with the curse of dimensionality presents another challenge due to the abundance of spectral and spatial information in each hyperspectral cube. State-of-the-art methods based on 1D and 2D convolutional neural networks (CNNs) struggle to efficiently extract spectral and spatial information. On the other hand, 3D-CNN-based models have shown significant promise in achieving better classification and detection results by leveraging spectral and spatial features simultaneously. Despite the apparent benefits of 3D-CNN-based models, their usage for classification purposes in this area of research has remained limited. This paper seeks to address this gap by reviewing 3D-CNN-based architectures and the typical deep learning pipeline, including preprocessing and visualization of results, for the classification of hyperspectral images of diseased and defective crops. Furthermore, we discuss open research areas and challenges when utilizing 3D-CNNs with HSI data."This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors."https://www.sciencedirect.com/science/article/pii/S277237552300145

Hardware / Software Architectural and Technological Exploration for Energy-Efficient and Reliable Biomedical Devices

Nowadays, the ubiquity of smart appliances in our everyday lives is increasingly strengthening the links between humans and machines. Beyond making our lives easier and more convenient, smart devices are now playing an important role in personalized healthcare delivery. This technological breakthrough is particularly relevant in a world where population aging and unhealthy habits have made non-communicable diseases the first leading cause of death worldwide according to international public health organizations. In this context, smart health monitoring systems termed Wireless Body Sensor Nodes (WBSNs), represent a paradigm shift in the healthcare landscape by greatly lowering the cost of long-term monitoring of chronic diseases, as well as improving patients' lifestyles. WBSNs are able to autonomously acquire biological signals and embed on-node Digital Signal Processing (DSP) capabilities to deliver clinically-accurate health diagnoses in real-time, even outside of a hospital environment. Energy efficiency and reliability are fundamental requirements for WBSNs, since they must operate for extended periods of time, while relying on compact batteries. These constraints, in turn, impose carefully designed hardware and software architectures for hosting the execution of complex biomedical applications. In this thesis, I develop and explore novel solutions at the architectural and technological level of the integrated circuit design domain, to enhance the energy efficiency and reliability of current WBSNs. Firstly, following a top-down approach driven by the characteristics of biomedical algorithms, I perform an architectural exploration of a heterogeneous and reconfigurable computing platform devoted to bio-signal analysis. By interfacing a shared Coarse-Grained Reconfigurable Array (CGRA) accelerator, this domain-specific platform can achieve higher performance and energy savings, beyond the capabilities offered by a baseline multi-processor system. More precisely, I propose three CGRA architectures, each contributing differently to the maximization of the application parallelization. The proposed Single, Multi and Interleaved-Datapath CGRA designs allow the developed platform to achieve substantial energy savings of up to 37%, when executing complex biomedical applications, with respect to a multi-core-only platform. Secondly, I investigate how the modeling of technology reliability issues in logic and memory components can be exploited to adequately adjust the frequency and supply voltage of a circuit, with the aim of optimizing its computing performance and energy efficiency. To this end, I propose a novel framework for workload-dependent Bias Temperature Instability (BTI) impact analysis on biomedical application results quality. Remarkably, the framework is able to determine the range of safe circuit operating frequencies without introducing worst-case guard bands. Experiments highlight the possibility to safely raise the frequency up to 101% above the maximum obtained with the classical static timing analysis. Finally, through the study of several well-known biomedical algorithms, I propose an approach allowing energy savings by dynamically and unequally protecting an under-powered data memory in a new way compared to regular error protection schemes. This solution relies on the Dynamic eRror compEnsation And Masking (DREAM) technique that reduces by approximately 21% the energy consumed by traditional error correction codes

Spectral-spatial classification of n-dimensional images in real-time based on segmentation and mathematical morphology on GPUs

The objective of this thesis is to develop efficient schemes for spectral-spatial n-dimensional image classification. By efficient schemes, we mean schemes that produce good classification results in terms of accuracy, as well as schemes that can be executed in real-time on low-cost computing infrastructures, such as the Graphics Processing Units (GPUs) shipped in personal computers. The n-dimensional images include images with two and three dimensions, such as images coming from the medical domain, and also images ranging from ten to hundreds of dimensions, such as the multiand hyperspectral images acquired in remote sensing. In image analysis, classification is a regularly used method for information retrieval in areas such as medical diagnosis, surveillance, manufacturing and remote sensing, among others. In addition, as the hyperspectral images have been widely available in recent years owing to the reduction in the size and cost of the sensors, the number of applications at lab scale, such as food quality control, art forgery detection, disease diagnosis and forensics has also increased. Although there are many spectral-spatial classification schemes, most are computationally inefficient in terms of execution time. In addition, the need for efficient computation on low-cost computing infrastructures is increasing in line with the incorporation of technology into everyday applications. In this thesis we have proposed two spectral-spatial classification schemes: one based on segmentation and other based on wavelets and mathematical morphology. These schemes were designed with the aim of producing good classification results and they perform better than other schemes found in the literature based on segmentation and mathematical morphology in terms of accuracy. Additionally, it was necessary to develop techniques and strategies for efficient GPU computing, for example, a block–asynchronous strategy, resulting in an efficient implementation on GPU of the aforementioned spectral-spatial classification schemes. The optimal GPU parameters were analyzed and different data partitioning and thread block arrangements were studied to exploit the GPU resources. The results show that the GPU is an adequate computing platform for on-board processing of hyperspectral information

OPTIMIZED ARCHITECTURE DESIGN AND IMPLEMENTATION OF OBJECT TRACKING ALGORITHM ON FPGA

FPGA based Object tracking implementation is one of the most recent video surveillance applications in embedded systems. In general, FPGA implementation is more efficient than general purpose computers in attaining high throughput due to its parallelism and execution speed. The system need to be designed on a standard frame rate in such a way to achieve optimal performance in real time environment. Optimal design of a system is dependent on minimizing the cost, area (device utility) and power while achieving the required speed. Past research work that investigated object tracking systems' implementation on FPGA achieved a significantly high throughput but have shown high device utilization. This research work aims at optimizing the device utilization under real time constraints. The Adaptive Hybrid Difference algorithm (AHD), which is used to detect the moving objects, was chosen to be implemented on FPGA due to its computation ability and efficiency with regard to hardware implementation. AHD can work at various lighting conditions automatically by determining the adaptive threshold in every period of time

Intraoperative tissue classification methods in orthopedic and neurological surgeries: A systematic review

Accurate tissue differentiation during orthopedic and neurological surgeries is critical, given that such surgeries involve operations on or in the vicinity of vital neurovascular structures and erroneous surgical maneuvers can lead to surgical complications. By now, the number of emerging technologies tackling the problem of intraoperative tissue classification methods is increasing. Therefore, this systematic review paper intends to give a general overview of existing technologies. The review was done based on the PRISMA principle and two databases: PubMed and IEEE Xplore. The screening process resulted in 60 full-text papers. The general characteristics of the methodology from extracted papers included data processing pipeline, machine learning methods if applicable, types of tissues that can be identified with them, phantom used to conduct the experiment, and evaluation results. This paper can be useful in identifying the problems in the current status of the state-of-the-art intraoperative tissue classification methods and designing new enhanced techniques

Deep Representation Learning with Limited Data for Biomedical Image Synthesis, Segmentation, and Detection

Biomedical imaging requires accurate expert annotation and interpretation that can aid medical staff and clinicians in automating differential diagnosis and solving underlying health conditions. With the advent of Deep learning, it has become a standard for reaching expert-level performance in non-invasive biomedical imaging tasks by training with large image datasets. However, with the need for large publicly available datasets, training a deep learning model to learn intrinsic representations becomes harder. Representation learning with limited data has introduced new learning techniques, such as Generative Adversarial Networks, Semi-supervised Learning, and Self-supervised Learning, that can be applied to various biomedical applications. For example, ophthalmologists use color funduscopy (CF) and fluorescein angiography (FA) to diagnose retinal degenerative diseases. However, fluorescein angiography requires injecting a dye, which can create adverse reactions in the patients. So, to alleviate this, a non-invasive technique needs to be developed that can translate fluorescein angiography from fundus images. Similarly, color funduscopy and optical coherence tomography (OCT) are also utilized to semantically segment the vasculature and fluid build-up in spatial and volumetric retinal imaging, which can help with the future prognosis of diseases. Although many automated techniques have been proposed for medical image segmentation, the main drawback is the model's precision in pixel-wise predictions. Another critical challenge in the biomedical imaging field is accurately segmenting and quantifying dynamic behaviors of calcium signals in cells. Calcium imaging is a widely utilized approach to studying subcellular calcium activity and cell function; however, large datasets have yielded a profound need for fast, accurate, and standardized analyses of calcium signals. For example, image sequences from calcium signals in colonic pacemaker cells ICC (Interstitial cells of Cajal) suffer from motion artifacts and high periodic and sensor noise, making it difficult to accurately segment and quantify calcium signal events. Moreover, it is time-consuming and tedious to annotate such a large volume of calcium image stacks or videos and extract their associated spatiotemporal maps. To address these problems, we propose various deep representation learning architectures that utilize limited labels and annotations to address the critical challenges in these biomedical applications. To this end, we detail our proposed semi-supervised, generative adversarial networks and transformer-based architectures for individual learning tasks such as retinal image-to-image translation, vessel and fluid segmentation from fundus and OCT images, breast micro-mass segmentation, and sub-cellular calcium events tracking from videos and spatiotemporal map quantification. We also illustrate two multi-modal multi-task learning frameworks with applications that can be extended to other domains of biomedical applications. The main idea is to incorporate each of these as individual modules to our proposed multi-modal frameworks to solve the existing challenges with 1) Fluorescein angiography synthesis, 2) Retinal vessel and fluid segmentation, 3) Breast micro-mass segmentation, and 4) Dynamic quantification of calcium imaging datasets

Visual inspection : image sampling, algorithms and architectures

The thesis concerns the hexagonal sampling of images, the processing of industrially derived images, and the design of a novel processor element that can be assembled into pipelines to effect fast, economic and reliable processing. A hexagonally sampled two dimensional image can require 13.4% fewer sampling points than a square sampled equivalent. The grid symmetry results in simpler processing operators that compute more efficiently than square grid operators. Computation savings approaching 44% arc demonstrated. New hexagonal operators arc reported including a Gaussian smoothing filter, a binary thinner, and an edge detector with comparable accuracy to that of the Sobel detector. The design of hexagonal arrays of sensors is considered. Operators requiring small local areas of support are shown to be sufficient for processing controlled lighting and industrial images. Case studies show that small features in hexagonally processed images maintain their shape better, and that processes can tolerate a lower signal to noise ratio, than that for equivalent square processed images. The modelling of small defects in surfaces has been studied in depth. The flexible programmable processor element can perform the low level local operators required for industrial image processing on both square and hexagonal grids. The element has been specified and simulated by a high level computer program. A fast communication channel allows for dynamic reprogramming by a control computer, and the video rate element can be assembled into various pipeline architectures, that may eventually be adaptively controlled

Fundus image analysis for automatic screening of ophthalmic pathologies

En los ultimos años el número de casos de ceguera se ha reducido significativamente. A pesar de este hecho, la Organización Mundial de la Salud estima que un 80% de los casos de pérdida de visión (285 millones en 2010) pueden ser evitados si se diagnostican en sus estadios más tempranos y son tratados de forma efectiva. Para cumplir esta propuesta se pretende que los servicios de atención primaria incluyan un seguimiento oftalmológico de sus pacientes así como fomentar campañas de cribado en centros proclives a reunir personas de alto riesgo. Sin embargo, estas soluciones exigen una alta carga de trabajo de personal experto entrenado en el análisis de los patrones anómalos propios de cada enfermedad. Por lo tanto, el desarrollo de algoritmos para la creación de sistemas de cribado automáticos juga un papel vital en este campo. La presente tesis persigue la identificacion automática del daño retiniano provocado por dos de las patologías más comunes en la sociedad actual: la retinopatía diabética (RD) y la degenaración macular asociada a la edad (DMAE). Concretamente, el objetivo final de este trabajo es el desarrollo de métodos novedosos basados en la extracción de características de la imagen de fondo de ojo y clasificación para discernir entre tejido sano y patológico. Además, en este documento se proponen algoritmos de pre-procesado con el objetivo de normalizar la alta variabilidad existente en las bases de datos publicas de imagen de fondo de ojo y eliminar la contribución de ciertas estructuras retinianas que afectan negativamente en la detección del daño retiniano. A diferencia de la mayoría de los trabajos existentes en el estado del arte sobre detección de patologías en imagen de fondo de ojo, los métodos propuestos a lo largo de este manuscrito evitan la necesidad de segmentación de las lesiones o la generación de un mapa de candidatos antes de la fase de clasificación. En este trabajo, Local binary patterns, perfiles granulométricos y la dimensión fractal se aplican de manera local para extraer información de textura, morfología y tortuosidad de la imagen de fondo de ojo. Posteriormente, esta información se combina de diversos modos formando vectores de características con los que se entrenan avanzados métodos de clasificación formulados para discriminar de manera óptima entre exudados, microaneurismas, hemorragias y tejido sano. Mediante diversos experimentos, se valida la habilidad del sistema propuesto para identificar los signos más comunes de la RD y DMAE. Para ello se emplean bases de datos públicas con un alto grado de variabilidad sin exlcuir ninguna imagen. Además, la presente tesis también cubre aspectos básicos del paradigma de deep learning. Concretamente, se presenta un novedoso método basado en redes neuronales convolucionales (CNNs). La técnica de transferencia de conocimiento se aplica mediante el fine-tuning de las arquitecturas de CNNs más importantes en el estado del arte. La detección y localización de exudados mediante redes neuronales se lleva a cabo en los dos últimos experimentos de esta tesis doctoral. Cabe destacar que los resultados obtenidos mediante la extracción de características "manual" y posterior clasificación se comparan de forma objetiva con las predicciones obtenidas por el mejor modelo basado en CNNs. Los prometedores resultados obtenidos en esta tesis y el bajo coste y portabilidad de las cámaras de adquisión de imagen de retina podrían facilitar la incorporación de los algoritmos desarrollados en este trabajo en un sistema de cribado automático que ayude a los especialistas en la detección de patrones anomálos característicos de las dos enfermedades bajo estudio: RD y DMAE.In last years, the number of blindness cases has been significantly reduced. Despite this promising news, the World Health Organisation estimates that 80% of visual impairment (285 million cases in 2010) could be avoided if diagnosed and treated early. To accomplish this purpose, eye care services need to be established in primary health and screening campaigns should be a common task in centres with people at risk. However, these solutions entail a high workload for trained experts in the analysis of the anomalous patterns of each eye disease. Therefore, the development of algorithms for automatic screening system plays a vital role in this field. This thesis focuses on the automatic identification of the retinal damage provoked by two of the most common pathologies in the current society: diabetic retinopathy (DR) and age-related macular degeneration (AMD). Specifically, the final goal of this work is to develop novel methods, based on fundus image description and classification, to characterise the healthy and abnormal tissue in the retina background. In addition, pre-processing algorithms are proposed with the aim of normalising the high variability of fundus images and removing the contribution of some retinal structures that could hinder in the retinal damage detection. In contrast to the most of the state-of-the-art works in damage detection using fundus images, the methods proposed throughout this manuscript avoid the necessity of lesion segmentation or the candidate map generation before the classification stage. Local binary patterns, granulometric profiles and fractal dimension are locally computed to extract texture, morphological and roughness information from retinal images. Different combinations of this information feed advanced classification algorithms formulated to optimally discriminate exudates, microaneurysms, haemorrhages and healthy tissues. Through several experiments, the ability of the proposed system to identify DR and AMD signs is validated using different public databases with a large degree of variability and without image exclusion. Moreover, this thesis covers the basics of the deep learning paradigm. In particular, a novel approach based on convolutional neural networks is explored. The transfer learning technique is applied to fine-tune the most important state-of-the-art CNN architectures. Exudate detection and localisation tasks using neural networks are carried out in the last two experiments of this thesis. An objective comparison between the hand-crafted feature extraction and classification process and the prediction models based on CNNs is established. The promising results of this PhD thesis and the affordable cost and portability of retinal cameras could facilitate the further incorporation of the developed algorithms in a computer-aided diagnosis (CAD) system to help specialists in the accurate detection of anomalous patterns characteristic of the two diseases under study: DR and AMD.En els últims anys el nombre de casos de ceguera s'ha reduït significativament. A pesar d'este fet, l'Organització Mundial de la Salut estima que un 80% dels casos de pèrdua de visió (285 milions en 2010) poden ser evitats si es diagnostiquen en els seus estadis més primerencs i són tractats de forma efectiva. Per a complir esta proposta es pretén que els servicis d'atenció primària incloguen un seguiment oftalmològic dels seus pacients així com fomentar campanyes de garbellament en centres regentats per persones d'alt risc. No obstant això, estes solucions exigixen una alta càrrega de treball de personal expert entrenat en l'anàlisi dels patrons anòmals propis de cada malaltia. Per tant, el desenrotllament d'algoritmes per a la creació de sistemes de garbellament automàtics juga un paper vital en este camp. La present tesi perseguix la identificació automàtica del dany retiniano provocat per dos de les patologies més comunes en la societat actual: la retinopatia diabètica (RD) i la degenaración macular associada a l'edat (DMAE) . Concretament, l'objectiu final d'este treball és el desenrotllament de mètodes novedodos basats en l'extracció de característiques de la imatge de fons d'ull i classificació per a discernir entre teixit sa i patològic. A més, en este document es proposen algoritmes de pre- processat amb l'objectiu de normalitzar l'alta variabilitat existent en les bases de dades publiques d'imatge de fons d'ull i eliminar la contribució de certes estructures retinianas que afecten negativament en la detecció del dany retiniano. A diferència de la majoria dels treballs existents en l'estat de l'art sobre detecció de patologies en imatge de fons d'ull, els mètodes proposats al llarg d'este manuscrit eviten la necessitat de segmentació de les lesions o la generació d'un mapa de candidats abans de la fase de classificació. En este treball, Local binary patterns, perfils granulometrics i la dimensió fractal s'apliquen de manera local per a extraure informació de textura, morfologia i tortuositat de la imatge de fons d'ull. Posteriorment, esta informació es combina de diversos modes formant vectors de característiques amb els que s'entrenen avançats mètodes de classificació formulats per a discriminar de manera òptima entre exsudats, microaneurismes, hemorràgies i teixit sa. Per mitjà de diversos experiments, es valida l'habilitat del sistema proposat per a identificar els signes més comuns de la RD i DMAE. Per a això s'empren bases de dades públiques amb un alt grau de variabilitat sense exlcuir cap imatge. A més, la present tesi també cobrix aspectes bàsics del paradigma de deep learning. Concretament, es presenta un nou mètode basat en xarxes neuronals convolucionales (CNNs) . La tècnica de transferencia de coneixement s'aplica per mitjà del fine-tuning de les arquitectures de CNNs més importants en l'estat de l'art. La detecció i localització d'exudats per mitjà de xarxes neuronals es du a terme en els dos últims experiments d'esta tesi doctoral. Cal destacar que els resultats obtinguts per mitjà de l'extracció de característiques "manual" i posterior classificació es comparen de forma objectiva amb les prediccions obtingudes pel millor model basat en CNNs. Els prometedors resultats obtinguts en esta tesi i el baix cost i portabilitat de les cambres d'adquisión d'imatge de retina podrien facilitar la incorporació dels algoritmes desenrotllats en este treball en un sistema de garbellament automàtic que ajude als especialistes en la detecció de patrons anomálos característics de les dos malalties baix estudi: RD i DMAE.Colomer Granero, A. (2018). Fundus image analysis for automatic screening of ophthalmic pathologies [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/99745TESI