New algorithms for the analysis of live-cell images acquired in phase contrast microscopy

La détection et la caractérisation automatisée des cellules constituent un enjeu important dans de nombreux domaines de recherche tels que la cicatrisation, le développement de l'embryon et des cellules souches, l’immunologie, l’oncologie, l'ingénierie tissulaire et la découverte de nouveaux médicaments. Étudier le comportement cellulaire in vitro par imagerie des cellules vivantes et par le criblage à haut débit implique des milliers d'images et de vastes quantités de données. Des outils d'analyse automatisés reposant sur la vision numérique et les méthodes non-intrusives telles que la microscopie à contraste de phase (PCM) sont nécessaires. Comme les images PCM sont difficiles à analyser en raison du halo lumineux entourant les cellules et de la difficulté à distinguer les cellules individuelles, le but de ce projet était de développer des algorithmes de traitement d'image PCM dans Matlab® afin d’en tirer de l’information reliée à la morphologie cellulaire de manière automatisée. Pour développer ces algorithmes, des séries d’images de myoblastes acquises en PCM ont été générées, en faisant croître les cellules dans un milieu avec sérum bovin (SSM) ou dans un milieu sans sérum (SFM) sur plusieurs passages. La surface recouverte par les cellules a été estimée en utilisant un filtre de plage de valeurs, un seuil et une taille minimale de coupe afin d'examiner la cinétique de croissance cellulaire. Les résultats ont montré que les cellules avaient des taux de croissance similaires pour les deux milieux de culture, mais que celui-ci diminue de façon linéaire avec le nombre de passages. La méthode de transformée par ondelette continue combinée à l’analyse d'image multivariée (UWT-MIA) a été élaborée afin d’estimer la distribution de caractéristiques morphologiques des cellules (axe majeur, axe mineur, orientation et rondeur). Une analyse multivariée réalisée sur l’ensemble de la base de données (environ 1 million d’images PCM) a montré d'une manière quantitative que les myoblastes cultivés dans le milieu SFM étaient plus allongés et plus petits que ceux cultivés dans le milieu SSM. Les algorithmes développés grâce à ce projet pourraient être utilisés sur d'autres phénotypes cellulaires pour des applications de criblage à haut débit et de contrôle de cultures cellulaires.Automated cell detection and characterization is important in many research fields such as wound healing, embryo development, immune system studies, cancer research, parasite spreading, tissue engineering, stem cell research and drug research and testing. Studying in vitro cellular behavior via live-cell imaging and high-throughput screening involves thousands of images and vast amounts of data, and automated analysis tools relying on machine vision methods and non-intrusive methods such as phase contrast microscopy (PCM) are a necessity. However, there are still some challenges to overcome, since PCM images are difficult to analyze because of the bright halo surrounding the cells and blurry cell-cell boundaries when they are touching. The goal of this project was to develop image processing algorithms to analyze PCM images in an automated fashion, capable of processing large datasets of images to extract information related to cellular viability and morphology. To develop these algorithms, a large dataset of myoblasts images acquired in live-cell imaging (in PCM) was created, growing the cells in either a serum-supplemented (SSM) or a serum-free (SFM) medium over several passages. As a result, algorithms capable of computing the cell-covered surface and cellular morphological features were programmed in Matlab®. The cell-covered surface was estimated using a range filter, a threshold and a minimum cut size in order to look at the cellular growth kinetics. Results showed that the cells were growing at similar paces for both media, but their growth rate was decreasing linearly with passage number. The undecimated wavelet transform multivariate image analysis (UWT-MIA) method was developed, and was used to estimate cellular morphological features distributions (major axis, minor axis, orientation and roundness distributions) on a very large PCM image dataset using the Gabor continuous wavelet transform. Multivariate data analysis performed on the whole database (around 1 million PCM images) showed in a quantitative manner that myoblasts grown in SFM were more elongated and smaller than cells grown in SSM. The algorithms developed through this project could be used in the future on other cellular phenotypes for high-throughput screening and cell culture control applications

Off-line Arabic Handwriting Recognition System Using Fast Wavelet Transform

In this research, off-line handwriting recognition system for Arabic alphabet is introduced. The system contains three main stages: preprocessing, segmentation and recognition stage. In the preprocessing stage, Radon transform was used in the design of algorithms for page, line and word skew correction as well as for word slant correction. In the segmentation stage, Hough transform approach was used for line extraction. For line to words and word to characters segmentation, a statistical method using mathematic representation of the lines and words binary image was used. Unlike most of current handwriting recognition system, our system simulates the human mechanism for image recognition, where images are encoded and saved in memory as groups according to their similarity to each other. Characters are decomposed into a coefficient vectors, using fast wavelet transform, then, vectors, that represent a character in different possible shapes, are saved as groups with one representative for each group. The recognition is achieved by comparing a vector of the character to be recognized with group representatives. Experiments showed that the proposed system is able to achieve the recognition task with 90.26% of accuracy. The system needs only 3.41 seconds a most to recognize a single character in a text of 15 lines where each line has 10 words on average

Advances in Sensors, Big Data and Machine Learning in Intelligent Animal Farming

Animal production (e.g., milk, meat, and eggs) provides valuable protein production for human beings and animals. However, animal production is facing several challenges worldwide such as environmental impacts and animal welfare/health concerns. In animal farming operations, accurate and efficient monitoring of animal information and behavior can help analyze the health and welfare status of animals and identify sick or abnormal individuals at an early stage to reduce economic losses and protect animal welfare. In recent years, there has been growing interest in animal welfare. At present, sensors, big data, machine learning, and artificial intelligence are used to improve management efficiency, reduce production costs, and enhance animal welfare. Although these technologies still have challenges and limitations, the application and exploration of these technologies in animal farms will greatly promote the intelligent management of farms. Therefore, this Special Issue will collect original papers with novel contributions based on technologies such as sensors, big data, machine learning, and artificial intelligence to study animal behavior monitoring and recognition, environmental monitoring, health evaluation, etc., to promote intelligent and accurate animal farm management

Off-line Arabic Handwriting Recognition System Using Fast Wavelet Transform

In this research, off-line handwriting recognition system for Arabic alphabet is introduced. The system contains three main stages: preprocessing, segmentation and recognition stage. In the preprocessing stage, Radon transform was used in the design of algorithms for page, line and word skew correction as well as for word slant correction. In the segmentation stage, Hough transform approach was used for line extraction. For line to words and word to characters segmentation, a statistical method using mathematic representation of the lines and words binary image was used. Unlike most of current handwriting recognition system, our system simulates the human mechanism for image recognition, where images are encoded and saved in memory as groups according to their similarity to each other. Characters are decomposed into a coefficient vectors, using fast wavelet transform, then, vectors, that represent a character in different possible shapes, are saved as groups with one representative for each group. The recognition is achieved by comparing a vector of the character to be recognized with group representatives. Experiments showed that the proposed system is able to achieve the recognition task with 90.26% of accuracy. The system needs only 3.41 seconds a most to recognize a single character in a text of 15 lines where each line has 10 words on average

Measuring Behavior 2018 Conference Proceedings

These proceedings contain the papers presented at Measuring Behavior 2018, the 11th International Conference on Methods and Techniques in Behavioral Research. The conference was organised by Manchester Metropolitan University, in collaboration with Noldus Information Technology. The conference was held during June 5th – 8th, 2018 in Manchester, UK. Building on the format that has emerged from previous meetings, we hosted a fascinating program about a wide variety of methodological aspects of the behavioral sciences. We had scientific presentations scheduled into seven general oral sessions and fifteen symposia, which covered a topical spread from rodent to human behavior. We had fourteen demonstrations, in which academics and companies demonstrated their latest prototypes. The scientific program also contained three workshops, one tutorial and a number of scientific discussion sessions. We also had scientific tours of our facilities at Manchester Metropolitan Univeristy, and the nearby British Cycling Velodrome. We hope this proceedings caters for many of your interests and we look forward to seeing and hearing more of your contributions

Pilot study for subgroup classification for autism spectrum disorder based on dysmorphology and physical measurements in Chinese children

Poster Sessions: 157 - Comorbid Medical Conditions: abstract 157.058 58BACKGROUND: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder affecting individuals along a continuum of severity in communication, social interaction and behaviour. The impact of ASD significantly varies amongst individuals, and the cause of ASD can originate broadly between genetic and environmental factors. Objectives: Previous ASD researches indicate that early identification combined with a targeted treatment plan involving behavioural interventions and multidisciplinary therapies can provide substantial improvement for ASD patients. Currently there is no cure for ASD, and the clinical variability and uncertainty of the disorder still remains. Hence, the search to unravel heterogeneity within ASD by subgroup classification may provide clinicians with a better understanding of ASD and to work towards a more definitive course of action. METHODS: In this study, a norm of physical measurements including height, weight, head circumference, ear length, outer and inner canthi, interpupillary distance, philtrum, hand and foot length was collected from 658 Typical Developing (TD) Chinese children aged 1 to 7 years (mean age of 4.19 years). The norm collected was compared against 80 ASD Chinese children aged 1 to 12 years (mean age of 4.36 years). We then further attempted to find subgroups within ASD based on identifying physical abnormalities; individuals were classified as (non) dysmorphic with the Autism Dysmorphology Measure (ADM) from physical examinations of 12 body regions. RESULTS: Our results show that there were significant differences between ASD and TD children for measurements in: head circumference (p=0.009), outer (p=0.021) and inner (p=0.021) canthus, philtrum length (p=0.003), right (p=0.023) and left (p=0.20) foot length. Within the 80 ASD patients, 37(46%) were classified as dysmorphic (p=0.00). CONCLUSIONS: This study attempts to identify subgroups within ASD based on physical measurements and dysmorphology examinations. The information from this study seeks to benefit ASD community by identifying possible subtypes of ASD in Chinese population; in seek for a more definitive diagnosis, referral and treatment plan.published_or_final_versio