Alvaro Rodriguez

Optical Fish Trajectory Measurement in Fishways through Computer Vision and Artificial Neural Networks

Vertical slot fishways are hydraulic structures that allow the upstream migration of fish through obstructions in rivers. The appropriate design of a vertical slot fishway depends on the interplay between hydraulic and biological variables because the hydrodynamic properties of the fishway must match the requirements of the fish species for which it is intended. One of the primary difficulties associated with studies of real fish behavior in fishway models is that the existing mechanisms to measure the behavior of the fish in these assays, such as direct observation or placement of sensors on the specimens, are impractical or unduly affect the animal behavior. This paper proposes a new procedure for measuring the behavior of the fish. The proposed technique uses artificial neural networks and computer vision techniques to analyze images obtained from the assays by means of a camera system designed for fishway integration. It is expected that this technique will provide detailed information about the fish behavior, and it will help to improve fish passage devices, which is currently a subject of interest in the area of civil engineering. A series of assays has been performed to validate this new approach in a full-scale fishway model with living fish. We have obtained very promising results that allow accurate reconstruction of the movements of the fish within the fishway.

Two-dimensional gel electrophoresis image registration using block-matching techniques and deformation models

Block-matching techniques have been widely used in the task of estimating displacement in medical images, and they represent the best approach in scenes with deformable structures such as tissues, fluids, and gels. In this article, a new iterative block-matching technique-based on successive deformation, search, fitting, filtering, and interpolation stages-is proposed to measure elastic displacements in two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) images. The proposed technique uses different deformation models in the task of correlating proteins in real 2D electrophoresis gel images, obtaining an accuracy of 96.6% and improving the results obtained with other techniques. This technique represents a general solution, being easy to adapt to different 2D deformable cases and providing an experimental reference for block-matching algorithms.

UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data

We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holog ...

Fish Monitoring and Sizing Using Computer Vision

This paper proposes an image processing algorithm, based in a non invasive 3D optical stereo system and the use of computer vision techniques, to study fish in fish tanks or pools.

Study of strength tests with computer vision techniques

Knowing the strain response of materials in strength tests is one of the main issues in construction and engineering fields. In these tests, information about displacements and strains is usually carried out using physical devices attached to the material. In this paper, the suitability of Computer Vision techniques to analyse strength tests without interfering with the assay is discussed and a new technique is proposed. This technique measures displacements and deformations from a video sequence of the assay. With this purpose a Block-Matching Optical Flow algorithm is integrated with a calibration process to extract the vectorfield from the displacement in the material. To evaluate the proposed technique, a synthetic image set and a real sequence from a strength tests were analysed.

Refining particle positions using circular symmetry

Particle and object tracking is gaining attention in industrial applications and is commonly applied in: colloidal, biophysical, ecological, and micro-fluidic research. Reliable tracking information is heavily dependent on the system under study and algorithms that correctly determine particle position between images. However, in a real environmental context with the presence of noise including particular or dissolved matter in water, and low and fluctuating light conditions, many algorithms fail to obtain reliable information. We propose a new algorithm, the Circular Symmetry algorithm (C-Sym), for detecting the position of a circular particle with high accuracy and precision in noisy conditions. The algorithm takes advantage of the spatial symmetry of the particle allowing for subpixel accuracy. We compare the proposed algorithm with four different methods using both synthetic and experimental datasets. The results show that C-Sym is the most accurate and precise algorithm when tracking micro-particles in all tested conditions and it has the potential for use in applications including tracking biota in their environment.

High Prevalence of Mycoplasma pneumoniae and Chlamydia pneumoniae in Children with Acute Respiratory Infections from Lima, Peru.

Background Mycoplasma pneumoniae and Chlamydia pneumoniae are atypical pathogens responsible for pneumonia and a leading cause of morbidity and mortality in low income countries. The study objective is to determine the prevalence of this pathogens in Peruvian children with acute respiratory infections. Methods A consecutive cross-sectional study was conducted in Lima, Peru from May 2009 to September 2010. A total of 675 children admitted with clinical diagnoses of acute respiratory infections were tested for Mycoplasma pneumoniae and Chlamydia pneumoniae detection by polymerase chain reaction (PCR), and clinical symptoms were registered by the attending physician. Results Mycoplasma pneumonia was detected in 25.19% (170/675) of nasopharyngeal samples and Chlamydia pneumonia in 10.52% (71/675). The most common symptoms in patients with these atypical pathogens were rhinorrhea, cough and fever. A higher prevalence of Mycoplasma pneumoniae cases were registered in summer, between December 2009 and March 2010. Conclusions Mycoplasma pneumoniae and Chlamydia pneumonia are a significant cause of morbidity in Peruvian children with acute respiratory infections (ARI). Further studies should evaluate the use of reliable techniques such as PCR in Peru in order to avoid underdiagnoses of these atypical pathogens.

ToxTrac: A fast and robust software for tracking organisms

1. Behavioral analysis based on video recording is becoming increasingly popular within research fields such as; ecology, medicine, ecotoxicology, and toxicology. However, the programs available to ...

Motion estimation in real deformation processes based on block-matching techniques

Non rigid motion estimation is one of the main issues in several fields, ranging from medical image analysis to civil engineering.

ToxId : an efficient algorithm to solve occlusions when tracking multiple animals

Video analysis of animal behaviour is widely used in fields such as ecology, ecotoxicology, and evolutionary research. However, when tracking multiple animals, occlusion and crossing are problematic, especially when the identity of each individual needs to be preserved. We present a new algorithm, ToxId, which preserves the identity of multiple animals by linking trajectory segments using their intensity histogram and Hu-moments. We verify the performance and accuracy of our algorithm using video sequences with different animals and experimental conditions. The results show that our algorithm achieves state-of-the-art accuracy using an efficient approach without the need of learning processes, complex feature maps or knowledge of the animal shape. ToxId is also computationally efficient, has low memory requirements, and operates without accessing future or past frames.