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- Illumination correction and analysis of two-dimensional microscopy images of Loa loa microfilariaePublication . Al-Tam, Faroq; Shahbazkia, Hamid Reza; Anjos, António dosThis thesis addresses the problem of detecting a common parasitic micro laria that causes loaisis, a major disease problem in Central and Western Africa. The dose of medicine to be administered to the patient is proportional to the estimated number of micro lariae in the patient's body. Therefore, proper estimation of the number of micro lariae is the key for conducting the right procedure. The clinical examination is necessary to estimate the micro lariae density in a blood sample drawn from the patient. Thereafter, visual inspection of the sample is performed. The main challenge in this work is, however, the development of an automatic detection system of micro lariae in 2-D images. Such problem is new in the image processing literature, and the development of such system is very important for performing better diagnosis and treatment of this disease and other similar diseases. A comprehensive review of, both generic and thin, object detectors in 2-D images is presented. A very robust method for microscopy image illumination correction is proposed, and a new powerful descriptor, the Hessian-Polar Context (HPC), for micro lariae is also introduced. These are then combined in a micro lariae detection system, where a simple, yet e cient, hypotheses generator is also presented. Additionally, several methods and applications for di erent image modalities are proposed. These involve a method and an application for the analysis of rice panicle in 2-D images. Additionally, an e cient method for artifact suppression in X-ray image is also proposed. The proposed methods are compared to a set of state-of-the-art methods. Experimental results show that the developed methods are great contributions to the microscopy and X-ray imaging elds.
- On load balancing via switch migration in software-defined networkingPublication . Correia, Noélia; Al-Tam, FaroqSwitch-controller assignment is an essential task in multi-controller software-defined networking. Static assignments are not practical because network dynamics are complex and difficult to predetermine. Since network load varies both in space and time, the mapping of switches to controllers should be adaptive to sudden changes in the network. To that end, switch migration plays an important role in maintaining dynamic switch-controller mapping. Migrating switches from overloaded to underloaded controllers brings flexibility and adaptability to the network but, at the same time, deciding which switches should be migrated to which controllers, while maintaining a balanced load in the network, is a challenging task. This work presents a heuristic approach with solution shaking to solve the switch migration problem. Shift and swap moves are incorporated within a search scheme. Every move is evaluated by how much benefititwillgivetoboththeimmigrationandoutmigrationcontrollers.Theexperimentalresultsshowthat theproposedapproachisabletooutweighthestate-of-artapproaches,andimprovetheloadbalancingresults up to≈ 14% in some scenarios when compared to the most recent approach. In addition, the results show that the proposed work is more robust to controller failure than the state-of-art methods.
- Fractional switch migration in multi-controller software-defined networkingPublication . Al-Tam, Faroq; Correia, NoéliaMapping switches to controllers in multi-controller software-defined networking (SDN) is still a hot research topic. Many factors have to be considered when establishing this mapping. Among them are the load balancing and mapping stability. Load balancing is important to improve resources utilization, and mapping stability reduces the control plane overhead created when exchanging information triggered by new mappings. This article presents a model for dynamic switch-controller mapping to achieve load balancing and minimize the number of new switch-controller assignments. To that end, for load balancing, flows from a switch are allowed to be handled by multiple controllers, and to increase assignment stability, the assignments at time t - 1 are taken into consideration when calculating the assignments at time t. The model is formulated as a convex quadratic programming problem, and the properties and feasibility of this model are mathematically analyzed. In addition, a heuristic algorithm is developed to deal with large-scale networks. The experimental results show the effectiveness of the proposed approach when compared to recent academic work, where the proposed model leads to a slight improvement in the load balancing and increases the stability of the switch-controller assignment by approximate to 91%. (C) 2019 Elsevier B.V. All rights reserved.
- Warping, matching and reporting 2-D electrophoresis protein gel imagesPublication . Al-Tam, Faroq; Shahbazkia, Hamid Reza; Anjos, António dosIn Proteomics, Differential Analysis is the method of studying 2-D Electrophoresis (2-DE) images by finding the differences. This method involves comparing the images’ spots in order to find the missing, unidentified, and/or misplaced proteins. The manual comparison by visual inspection is a labor-intensive and error-prone task. Matching two gels is not an easy task. Biologists have to identify and quantify the spots one-by-one.
- P-TRAP: a Panicle Trait Phenotyping toolPublication . Al-Tam, Faroq; Adam, Helene; Dos Anjos, António; Lorieux, Mathias; Larmande, Pierre; Ghesquiere, Alain; Jouannic, Stefan; Shahbazkia, Hamid RezaBackground: In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results: This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions: P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.
- Iterative illumination correction with implicit regularizationPublication . Al-Tam, Faroq; Dos Anjos, António; Shahbazkia, Hamid RezaThis paper presents a retrospective algorithm for correcting the uneven illumination field in microscopy images. The illumination field is iteratively made uniform using an increasing sequence of bivariate polynomials. At each iteration, the least squares problem of fitting a 2-D polynomial to a sampled image is solved by using QR decomposition with column pivoting, where image samples are obtained by dynamic programming or watershed transform. This incremental scheme allows the smoothness constraint of the estimated bias field to be implicitly satisfied. The proper number of iterations is determined by an automatic stopping criterion. The experimental results show the effectiveness of the proposed approach when compared to a set of different well-established methods.
- DNAGear: a free software for spa type identification in Staphylococcus aureusPublication . Al-Tam, Faroq; Brunel, Anne-Sophie; Bouzinbi, Nicolas; Corne, Philippe; Bañuls, Anne-Laure; Shahbazkia, Hamid RezaStaphylococcus aureus is both human commensal and an important human pathogen, responsible for community-acquired and nosocomial infections ranging from superficial wound infections to invasive infections, such as osteomyelitis, bacteremia and endocarditis, pneumonia or toxin shock syndrome with a mortality rate up to 40%. S. aureus reveals a high genetic polymorphism and detecting the genotypes is extremely useful to manage and prevent possible outbreaks and to understand the route of infection. One of current and expanded typing method is based on the X region of the spa gene composed of a succession of repeats of 21 to 27 bp. More than 10000 types are known. Extracting the repeats is impossible by hand and needs a dedicated software. Unfortunately the only software on the market is a commercial program from Ridom. Findings This article presents DNAGear, a free and open source software with a user friendly interface written all in Java on top of NetBeans Platform to perform spa typing, detecting new repeats and new spa types and synchronizing automatically the files with the open access database. The installation is easy and the application is platform independent. In fact, the SPA identification is a formal regular expression matching problem and the results are 100% exact. As the program is using Java embedded modules written over string manipulation of well established algorithms, the exactitude of the solution is perfectly established. Conclusions DNAGear is able to identify the types of the S. aureus sequences and detect both new types and repeats. Comparing to manual processing, which is time consuming and error prone, this application saves a lot of time and effort and gives very reliable results. Additionally, the users do not need to prepare the forward-reverse sequences manually, or even by using additional tools. They can simply create them in DNAGear and perform the typing task. In short, researchers who do not have commercial software will benefit a lot from this application.