A Mixed Data-Based Deep Neural Network to Estimate Leaf Area Index in Wheat Breeding Trials

Remote and non-destructive estimation of leaf area index (LAI) has been a challenge in the last few decades as the direct and indirect methods available are laborious and time-consuming. The recent emergence of high-throughput plant phenotyping platforms has increased the need to develop new phenotyping tools for better decision-making by breeders. In this paper, a novel model based on artificial intelligence algorithms and nadir-view red green blue (RGB) images taken from a terrestrial high throughput phenotyping platform is presented. The model mixes numerical data collected in a wheat breeding field and visual features extracted from the images to make rapid and accurate LAI estimations. Model-based LAI estimations were validated against LAI measurements determined non-destructively using an allometric relationship obtained in this study. The model performance was also compared with LAI estimates obtained by other classical indirect methods based on bottom-up hemispherical images and gaps fraction theory. Model-based LAI estimations were highly correlated with ground-truth LAI. The model performance was slightly better than that of the hemispherical image-based method, which tended to underestimate LAI. These results show the great potential of the developed model for near real-time LAI estimation, which can be further improved in the future by increasing the dataset used to train the model

Deep Learning Approach for Large-Scale, Real-Time Quantification of Green Fluorescent Protein-Labeled Biological Samples in Microreactors

Absolute quantification of biological samples entails determining expression levels in precise numerical copies, offering enhanced accuracy and superior performance for rare templates. However, existing methodologies suffer from significant limitations: flow cytometers are both costly and intricate, while fluorescence imaging relying on software tools or manual counting is time-consuming and prone to inaccuracies. In this study, we have devised a comprehensive deep-learning-enabled pipeline that enables the automated segmentation and classification of GFP (green fluorescent protein)-labeled microreactors, facilitating real-time absolute quantification. Our findings demonstrate the efficacy of this technique in accurately predicting the sizes and occupancy status of microreactors using standard laboratory fluorescence microscopes, thereby providing precise measurements of template concentrations. Notably, our approach exhibits an analysis speed of quantifying over 2,000 microreactors (across 10 images) within remarkably 2.5 seconds, and a dynamic range spanning from 56.52 to 1569.43 copies per micron-liter. Furthermore, our Deep-dGFP algorithm showcases remarkable generalization capabilities, as it can be directly applied to various GFP-labeling scenarios, including droplet-based, microwell-based, and agarose-based biological applications. To the best of our knowledge, this represents the first successful implementation of an all-in-one image analysis algorithm in droplet digital PCR (polymerase chain reaction), microwell digital PCR, droplet single-cell sequencing, agarose digital PCR, and bacterial quantification, without necessitating any transfer learning steps, modifications, or retraining procedures. We firmly believe that our Deep-dGFP technique will be readily embraced by biomedical laboratories and holds potential for further development in related clinical applications.Comment: 23 pages, 6 figures, 1 tabl

Microservices and Machine Learning Algorithms for Adaptive Green Buildings

In recent years, the use of services for Open Systems development has consolidated and strengthened. Advances in the Service Science and Engineering (SSE) community, promoted by the reinforcement of Web Services and Semantic Web technologies and the presence of new Cloud computing techniques, such as the proliferation of microservices solutions, have allowed software architects to experiment and develop new ways of building open and adaptable computer systems at runtime. Home automation, intelligent buildings, robotics, graphical user interfaces are some of the social atmosphere environments suitable in which to apply certain innovative trends. This paper presents a schema for the adaptation of Dynamic Computer Systems (DCS) using interdisciplinary techniques on model-driven engineering, service engineering and soft computing. The proposal manages an orchestrated microservices schema for adapting component-based software architectural systems at runtime. This schema has been developed as a three-layer adaptive transformation process that is supported on a rule-based decision-making service implemented by means of Machine Learning (ML) algorithms. The experimental development was implemented in the Solar Energy Research Center (CIESOL) applying the proposed microservices schema for adapting home architectural atmosphere systems on Green Buildings

RF Localization in Indoor Environment

In this paper indoor localization system based on the RF power measurements of the Received Signal Strength (RSS) in WLAN environment is presented. Today, the most viable solution for localization is the RSS fingerprinting based approach, where in order to establish a relationship between RSS values and location, different machine learning approaches are used. The advantage of this approach based on WLAN technology is that it does not need new infrastructure (it reuses already and widely deployed equipment), and the RSS measurement is part of the normal operating mode of wireless equipment. We derive the Cramer-Rao Lower Bound (CRLB) of localization accuracy for RSS measurements. In analysis of the bound we give insight in localization performance and deployment issues of a localization system, which could help designing an efficient localization system. To compare different machine learning approaches we developed a localization system based on an artificial neural network, k-nearest neighbors, probabilistic method based on the Gaussian kernel and the histogram method. We tested the developed system in real world WLAN indoor environment, where realistic RSS measurements were collected. Experimental comparison of the results has been investigated and average location estimation error of around 2 meters was obtained

QuantiMus: A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology.

Skeletal muscle injury provokes a regenerative response, characterized by the de novo generation of myofibers that are distinguished by central nucleation and re-expression of developmentally restricted genes. In addition to these characteristics, myofiber cross-sectional area (CSA) is widely used to evaluate muscle hypertrophic and regenerative responses. Here, we introduce QuantiMus, a free software program that uses machine learning algorithms to quantify muscle morphology and molecular features with high precision and quick processing-time. The ability of QuantiMus to define and measure myofibers was compared to manual measurement or other automated software programs. QuantiMus rapidly and accurately defined total myofibers and measured CSA with comparable performance but quantified the CSA of centrally-nucleated fibers (CNFs) with greater precision compared to other software. It additionally quantified the fluorescence intensity of individual myofibers of human and mouse muscle, which was used to assess the distribution of myofiber type, based on the myosin heavy chain isoform that was expressed. Furthermore, analysis of entire quadriceps cross-sections of healthy and mdx mice showed that dystrophic muscle had an increased frequency of Evans blue dye+ injured myofibers. QuantiMus also revealed that the proportion of centrally nucleated, regenerating myofibers that express embryonic myosin heavy chain (eMyHC) or neural cell adhesion molecule (NCAM) were increased in dystrophic mice. Our findings reveal that QuantiMus has several advantages over existing software. The unique self-learning capacity of the machine learning algorithms provides superior accuracy and the ability to rapidly interrogate the complete muscle section. These qualities increase rigor and reproducibility by avoiding methods that rely on the sampling of representative areas of a section. This is of particular importance for the analysis of dystrophic muscle given the "patchy" distribution of muscle pathology. QuantiMus is an open source tool, allowing customization to meet investigator-specific needs and provides novel analytical approaches for quantifying muscle morphology

Integrated process of images and acceleration measurements for damage detection

The use of mobile robots and UAV to catch unthinkable images together with on-site global automated acceleration measurements easy achievable by wireless sensors, able of remote data transfer, have strongly enhanced the capability of defect and damage evaluation in bridges. A sequential procedure is, here, proposed for damage monitoring and bridge condition assessment based on both: digital image processing for survey and defect evaluation and structural identification based on acceleration measurements. A steel bridge has been simultaneously inspected by UAV to acquire images using visible light, or infrared radiation, and monitored through a wireless sensor network (WSN) measuring structural vibrations. First, image processing has been used to construct a geometrical model and to quantify corrosion extension. Then, the consistent structural model has been updated based on the modal quantities identified using the acceleration measurements acquired by the deployed WSN. © 2017 The Authors. Published by Elsevier Ltd

Understanding Health and Disease with Multidimensional Single-Cell Methods

Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in characteristic length scales, from small molecules that regulate cell function to cell ensembles that form tissues and organs working together as an organism. In order to uncover the molecular nature of the emergent properties of a cell, it is essential to measure multiple cell components simultaneously in the same cell. In turn, cell heterogeneity requires multiple cells to be measured in order to understand health and disease in the organism. This review summarizes current efforts towards a data-driven framework that leverages single-cell technologies to build robust signatures of healthy and diseased phenotypes. While some approaches focus on multicolor flow cytometry data and other methods are designed to analyze high-content image-based screens, we emphasize the so-called Supercell/SVM paradigm (recently developed by the authors of this review and collaborators) as a unified framework that captures mesoscopic-scale emergence to build reliable phenotypes. Beyond their specific contributions to basic and translational biomedical research, these efforts illustrate, from a larger perspective, the powerful synergy that might be achieved from bringing together methods and ideas from statistical physics, data mining, and mathematics to solve the most pressing problems currently facing the life sciences.Comment: 25 pages, 7 figures; revised version with minor changes. To appear in J. Phys.: Cond. Mat

Evaluation of Variability Concepts for Simulink in the Automotive Domain

Modeling variability in Matlab/Simulink becomes more and more important. We took the two variability modeling concepts already included in Matlab/Simulink and our own one and evaluated them to find out which one is suited best for modeling variability in the automotive domain. We conducted a controlled experiment with developers at Volkswagen AG to decide which concept is preferred by developers and if their preference aligns with measurable performance factors. We found out that all existing concepts are viable approaches and that the delta approach is both the preferred concept as well as the objectively most efficient one, which makes Delta-Simulink a good solution to model variability in the automotive domain.Comment: 10 pages, 7 figures, 6 tables, Proceedings of 48th Hawaii International Conference on System Sciences (HICSS), pp. 5373-5382, Kauai, Hawaii, USA, IEEE Computer Society, 201