A novel method for measuring lag times in division of individual bacterial cells using image analysis

A method is presented for determining the time to first division of individual bacterial cells growing on agar media. Bacteria were inoculated onto agar-coated slides and viewed by phase-contrast microscopy. Digital images of the growing bacteria were captured at intervals and the time to first division estimated by calculating the "box area ratio". This is the area of the smallest rectangle that can be drawn around an object, divided by the area of the object itself. The box area ratios of cells were found to increase suddenly during growth at a time that correlated with cell division as estimated by visual inspection of the digital images. This was caused by a change in the orientation of the two daughter cells that occurred when sufficient flexibility arose at their point of attachment. This method was used successfully to generate lag time distributions for populations of Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa, but did not work with the coccoid organism Staphylococcus aureus. This method provides an objective measure of the time to first cell division, whilst automation of the data processing allows a large number of cells to be examined per experiment. (c) 2005 Elsevier B.V. All rights reserved.

Maude Object-Oriented Action Tool

MAIDL, André Murbach; CARVILHE, Claudio; MUSICANTE, Martin A. Maude Object-Oriented Action Tool. Electronic Notes in Theoretical Computer Science. [S.l:s.n], 2008.

Image analysis in the morphological and morphometric study of teeth

The subject of this doctoral dissertation concerns the definition of a new methodology for the morphological and morphometric study of fossilized human teeth, and therefore strives to provide a contribution to the reconstruction of human evolutionary history that proposes to extend to the different species of hominid fossils. Standardized investigative methodologies are lacking both regarding the orientation of teeth subject to study and in the analysis that can be carried out on these teeth once they are oriented. The opportunity to standardize a primary analysis methodology is furnished by the study of certain early Neanderthal and preneanderthal molars recovered in two caves in southern Italy [Grotta Taddeo (Taddeo Cave) and Grotta del Poggio (Poggio Cave), near Marina di Camerata, Campania]. To these we can add other molars of Neanderthal and modern man of the upper Paleolithic era, specifically scanned in the paleoanthropology laboratory of the University of Arkansas (Fayetteville, Arkansas, USA), in order to increase the paleoanthropological sample data and thereby make the final results of the analyses more significant. The new analysis methodology is rendered as follows: 1. Standardization of an orientation system for primary molars (superior and inferior), starting from a scan of a sample of 30 molars belonging to modern man (15 M1 inferior and 15 M1 superior), the definition of landmarks, the comparison of various systems and the choice of a system of orientation for each of the two dental typologies. 2. The definition of an analysis procedure that considers only the first 4 millimeters of the dental crown starting from the collar: 5 sections parallel to the plane according to which the tooth has been oriented are carried out, spaced 1 millimeter between them. The intention is to determine a method that allows for the differentiation of fossilized species even in the presence of worn teeth. 3. Results and Conclusions. The new approach to the study of teeth provides a considerable quantity of information that can better be evaluated by increasing the fossil sample data. It has been demonstrated to be a valid tool in evolutionary classification that has allowed (us) to differentiate the Neanderthal sample from that of modern man. In a particular sense the molars of Grotta Taddeo, which up until this point it has not been possible to determine with exactness their species of origin, through the present research they are classified as Neanderthal.

Image Analysis Methods for Sugar Beet Phenotyping

In un mondo che richiede sempre maggiormente un'automazione delle attività della catena produttiva industriale, la computer vision rappresenta uno strumento fondamentale perciò che viene già riconosciuta internazionalmente come la Quarta Rivoluzione Industriale o Industry 4.0. Avvalendomi di questo strumento ho intrapreso presso l'azienda Syngenta lo studio della problematica della conta automatica del numero di foglie di una pianta. Il problema è stato affrontato utilizzando due differenti approcci, ispirandosi alla letteratura. All'interno dell'elaborato è presente anche la descrizione progettuale di un ulteriore metodo, ad oggi non presente in letteratura. Le metodologie saranno spiegate in dettaglio ed i risultati ottenuti saranno confrontati utilizzando i primi due approcci. Nel capitolo finale si trarranno le conclusioni sulle basi dei risultati ottenuti e dall'analisi degli stessi.

Context Aware e-Learning Objects and their Types from the Perspective of the Object-Oriented Paradigm

The contribution of this article demonstrates how to identify context-aware types of e-Learning objects (eLOs) derived from the subject domains. This perspective is taken from an engineering point of view and is applied during requirements elicitation and analysis relating to present work in constructing an object-oriented (OO), dynamic, and adaptive model to build and deliver packaged e-Learning courses. Consequently, three preliminary subject domains are presented and, as a result, three primitive types of eLOs are posited. These types educed from the subject domains are of structural, conceptual, and granular nature. Structural objects are responsible for the course itself, conceptual objects incorporate adaptive and logical interoperability, while granular objects congregate granular assets. Their differences, interrelationships, and responsibilities are discussed. A major design challenge relates to adaptive behaviour. Future research addresses refinement on the subject domains and adaptive hypermedia systems.

Land Cover Mapping by an Optimized Object-Oriented Approach. Case of Study Mediterranean Landscapes

Remote sensing information from spaceborne and airborne platforms continues to provide valuable data for different environmental monitoring applications. In this sense, high spatial resolution im-agery is an important source of information for land cover mapping. For the processing of high spa-tial resolution images, the object-based methodology is one of the most commonly used strategies. However, conventional pixel-based methods, which only use spectral information for land cover classification, are inadequate for classifying this type of images. This research presents a method-ology to characterise Mediterranean land covers in high resolution aerial images by means of an object-oriented approach. It uses a self-calibrating multi-band region growing approach optimised by pre-processing the image with a bilateral filtering. The obtained results show promise in terms of both segmentation quality and computational efficiency.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Design of an expandable manufacturing simulator through the application of object-oriented principles

In analysing manufacturing systems, for either design or operational reasons, failure to account for the potentially significant dynamics could produce invalid results. There are many analysis techniques that can be used, however, simulation is unique in its ability to assess detailed, dynamic behaviour. The use of simulation to analyse manufacturing systems would therefore seem appropriate if not essential. Many simulation software products are available but their ease of use and scope of application vary greatly. This is illustrated at one extreme by simulators which offer rapid but limited application whilst at the other simulation languages which are extremely flexible but tedious to code. Given that a typical manufacturing engineer does not posses in depth programming and simulation skills then the use of simulators over simulation languages would seem a more appropriate choice. Whilst simulators offer ease of use their limited functionality may preclude their use in many applications. The construction of current simulators makes it difficult to amend or extend the functionality of the system to meet new challenges. Some simulators could even become obsolete as users, demand modelling functionality that reflects the latest manufacturing system design and operation concepts. This thesis examines the deficiencies in current simulation tools and considers whether they can be overcome by the application of object-oriented principles. Object-oriented techniques have gained in popularity in recent years and are seen as having the potential to overcome any of the problems traditionally associated with software construction. There are a number of key concepts that are exploited in the work described in this thesis: the use of object-oriented techniques to act as a framework for abstracting engineering concepts into a simulation tool and the ability to reuse and extend object-oriented software. It is argued that current object-oriented simulation tools are deficient and that in designing such tools, object -oriented techniques should be used not just for the creation of individual simulation objects but for the creation of the complete software. This results in the ability to construct an easy to use simulator that is not limited by its initial functionality. The thesis presents the design of an object-oriented data driven simulator which can be freely extended. Discussion and work is focused on discrete parts manufacture. The system developed retains the ease of use typical of data driven simulators. Whilst removing any limitation on its potential range of applications. Reference is given to additions made to the simulator by other developers not involved in the original software development. Particular emphasis is put on the requirements of the manufacturing engineer and the need for Ihe engineer to carrv out dynamic evaluations.

A stereo-image analysis JAVA software with links to executable and source code

Scientists planning to use underwater stereoscopic image technologies are often faced with numerous problems during the methodological implementations: commercial equipment is too expensive; the setup or calibration is too complex; or the imaging processing (i.e. measuring objects in the stereo-images) is too complicated to be performed without a time-consuming phase of training and evaluation. The present paper addresses some of these problems and describes a workflow for stereoscopic measurements for marine biologists. It also provides instructions on how to assemble an underwater stereo-photographic system with two digital consumer cameras and gives step-by-step guidelines for setting up the hardware. The second part details a software procedure to correct stereo-image pairs for lens distortions, which is especially important when using cameras with non-calibrated optical units. The final part presents a guide to the process of measuring the lengths (or distances) of objects in stereoscopic image pairs. To reveal the applicability and the restrictions of the described systems and to test the effects of different types of camera (a compact camera and an SLR type), experiments were performed to determine the precision and accuracy of two generic stereo-imaging units: a diver-operated system based on two Olympus Mju 1030SW compact cameras and a cable-connected observatory system based on two Canon 1100D SLR cameras. In the simplest setup without any correction for lens distortion, the low-budget Olympus Mju 1030SW system achieved mean accuracy errors (percentage deviation of a measurement from the object's real size) between 10.2 and -7.6% (overall mean value: -0.6%), depending on the size, orientation and distance of the measured object from the camera. With the single lens reflex (SLR) system, very similar values between 10.1% and -3.4% (overall mean value: -1.2%) were observed. Correction of the lens distortion significantly improved the mean accuracy errors of either system. Even more, system precision (spread of the accuracy) improved significantly in both systems. Neither the use of a wide-angle converter nor multiple reassembly of the system had a significant negative effect on the results. The study shows that underwater stereophotography, independent of the system, has a high potential for robust and non-destructive in situ sampling and can be used without prior specialist training.

Maude Object-Oriented Action Tool

MAIDL, André Murbach; CARVILHE, Claudio; MUSICANTE, Martin A. Maude Object-Oriented Action Tool. Electronic Notes in Theoretical Computer Science. [S.l:s.n], 2008.

Maude Object-Oriented Action Tool

MAIDL, André Murbach; CARVILHE, Claudio; MUSICANTE, Martin A. Maude Object-Oriented Action Tool. Electronic Notes in Theoretical Computer Science. [S.l:s.n], 2008.

Evaluation of follicular lymphoid depletion in the Bursa of Fabricius: an alternative methodology using digital image analysis and artificial neural networks

Fifty Bursa of Fabricius (BF) were examined by conventional optical microscopy and digital images were acquired and processed using Matlab® 6.5 software. The Artificial Neuronal Network (ANN) was generated using Neuroshell® Classifier software and the optical and digital data were compared. The ANN was able to make a comparable classification of digital and optical scores. The use of ANN was able to classify correctly the majority of the follicles, reaching sensibility and specificity of 89% and 96%, respectively. When the follicles were scored and grouped in a binary fashion the sensibility increased to 90% and obtained the maximum value for the specificity of 92%. These results demonstrate that the use of digital image analysis and ANN is a useful tool for the pathological classification of the BF lymphoid depletion. In addition it provides objective results that allow measuring the dimension of the error in the diagnosis and classification therefore making comparison between databases feasible.

Chrysotile effects on human lung cell carcinoma in culture: 3-D reconstruction and DNA quantification by image analysis

Background: Chrysotile is considered less harmful to human health than other types of asbestos fibers. Its clearance from the lung is faster and, in comparison to amphibole forms of asbestos, chrysotile asbestos fail to accumulate in the lung tissue due to a mechanism involving fibers fragmentation in short pieces. Short exposure to chrysotile has not been associated with any histopathological alteration of lung tissue. Methods: The present work focuses on the association of small chrysotile fibers with interphasic and mitotic human lung cancer cells in culture, using for analyses confocal laser scanning microscopy and 3D reconstructions. The main goal was to perform the analysis of abnormalities in mitosis of fibers-containing cells as well as to quantify nuclear DNA content of treated cells during their recovery in fiber-free culture medium. Results: HK2 cells treated with chrysotile for 48 h and recovered in additional periods of 24, 48 and 72 h in normal medium showed increased frequency of multinucleated and apoptotic cells. DNA ploidy of the cells submitted to the same chrysotile treatment schedules showed enhanced aneuploidy values. The results were consistent with the high frequency of multipolar spindles observed and with the presence of fibers in the intercellular bridge during cytokinesis. Conclusion: The present data show that 48 h chrysotile exposure can cause centrosome amplification, apoptosis and aneuploid cell formation even when long periods of recovery were provided. Internalized fibers seem to interact with the chromatin during mitosis, and they could also interfere in cytokinesis, leading to cytokinesis failure which forms aneuploid or multinucleated cells with centrosome amplification.

Characterization of micro-bubble size distribution and flow configuration in DAF contact zone by a non-intrusive image analysis system and tracer tests

This paper aims to investigate the influence of some dissolved air flotation (DAF) process variables (specifically: the hydraulic detention time in the contact zone and the supplied dissolved air concentration) and the pH values, as pretreatment chemical variables, on the micro-bubble size distribution (BSD) in a DAF contact zone. This work was carried out in a pilot plant where bubbles were measured by an appropriate non-intrusive image acquisition system. The results show that the obtained diameter ranges were in agreement with values reported in the literature (10-100mm), quite independently of the investigated conditions. The linear average diameter varied from 20 to 30mm, or equivalently, the Sauter (d(3,2)) diameter varied from 40 to 50mm. In all investigated conditions, D(50) was between 75% and 95%. The BSD might present different profile (with a bimodal curve trend), however, when analyzing the volumetric frequency distribution (in some cases with the appearance of peaks in diameters ranging from 90-100mm). Regarding volumetric frequency analysis, all the investigated parameters can modify the BSD in DAF contact zone after the release point, thus potentially causing changes in DAF kinetics. This finding prompts further research in order to verify the effect of these BSD changes on solid particle removal efficiency by DAF.