Two-Dimensional Gel Electrophoresis Image Registration Using Block-Matching Techniques and Deformation Models

[Abstract] 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.Galicia. Consellería de Economía e Industria; 10MDS014CTGalicia. Consellería de Economía e Industria; 10SIN105004PRInstituto de Salud Carlos III; PI13/0028

Multimodal Three Dimensional Scene Reconstruction, The Gaussian Fields Framework

The focus of this research is on building 3D representations of real world scenes and objects using different imaging sensors. Primarily range acquisition devices (such as laser scanners and stereo systems) that allow the recovery of 3D geometry, and multi-spectral image sequences including visual and thermal IR images that provide additional scene characteristics. The crucial technical challenge that we addressed is the automatic point-sets registration task. In this context our main contribution is the development of an optimization-based method at the core of which lies a unified criterion that solves simultaneously for the dense point correspondence and transformation recovery problems. The new criterion has a straightforward expression in terms of the datasets and the alignment parameters and was used primarily for 3D rigid registration of point-sets. However it proved also useful for feature-based multimodal image alignment. We derived our method from simple Boolean matching principles by approximation and relaxation. One of the main advantages of the proposed approach, as compared to the widely used class of Iterative Closest Point (ICP) algorithms, is convexity in the neighborhood of the registration parameters and continuous differentiability, allowing for the use of standard gradient-based optimization techniques. Physically the criterion is interpreted in terms of a Gaussian Force Field exerted by one point-set on the other. Such formulation proved useful for controlling and increasing the region of convergence, and hence allowing for more autonomy in correspondence tasks. Furthermore, the criterion can be computed with linear complexity using recently developed Fast Gauss Transform numerical techniques. In addition, we also introduced a new local feature descriptor that was derived from visual saliency principles and which enhanced significantly the performance of the registration algorithm. The resulting technique was subjected to a thorough experimental analysis that highlighted its strength and showed its limitations. Our current applications are in the field of 3D modeling for inspection, surveillance, and biometrics. However, since this matching framework can be applied to any type of data, that can be represented as N-dimensional point-sets, the scope of the method is shown to reach many more pattern analysis applications

Identifying and Tracking Pedestrians Based on Sensor Fusion and Motion Stability Predictions

The lack of trustworthy sensors makes development of Advanced Driver Assistance System (ADAS) applications a tough task. It is necessary to develop intelligent systems by combining reliable sensors and real-time algorithms to send the proper, accurate messages to the drivers. In this article, an application to detect and predict the movement of pedestrians in order to prevent an imminent collision has been developed and tested under real conditions. The proposed application, first, accurately measures the position of obstacles using a two-sensor hybrid fusion approach: a stereo camera vision system and a laser scanner. Second, it correctly identifies pedestrians using intelligent algorithms based on polylines and pattern recognition related to leg positions (laser subsystem) and dense disparity maps and u-v disparity (vision subsystem). Third, it uses statistical validation gates and confidence regions to track the pedestrian within the detection zones of the sensors and predict their position in the upcoming frames. The intelligent sensor application has been experimentally tested with success while tracking pedestrians that cross and move in zigzag fashion in front of a vehicle

Multi Cost Function Fuzzy Stereo Matching Algorithm for Object Detection and Robot Motion Control

Stereo matching algorithms work with multiple images of a scene, taken from two viewpoints, to generate depth information. Authors usually use a single matching function to generate similarity between corresponding regions in the images. In the present research, the authors have considered a combination of multiple data costs for disparity generation. Disparity maps generated from stereo images tend to have noisy sections. The presented research work is related to a methodology to refine such disparity maps such that they can be further processed to detect obstacle regions.  A novel entropy based selective refinement (ESR) technique is proposed to refine the initial disparity map. The information from both the left disparity and right disparity maps are used for this refinement technique. For every disparity map, block wise entropy is calculated. The average entropy values of the corresponding positions in the disparity maps are compared. If the variation between these entropy values exceeds a threshold, then the corresponding disparity value is replaced with the mean disparity of the block with lower entropy. The results of this refinement are compared with similar methods and was observed to be better. Furthermore, in this research work, the v-disparity values are used to highlight the road surface in the disparity map. The regions belonging to the sky are removed through HSV based segmentation. The remaining regions which are our ROIs, are refined through a u-disparity area-based technique.  Based on this, the closest obstacles are detected through the use of k-means segmentation.  The segmented regions are further refined through a u-disparity image information-based technique and used as masks to highlight obstacle regions in the disparity maps. This information is used in conjunction with a kalman filter based path planning algorithm to guide a mobile robot from a source location to a destination location while also avoiding any obstacle detected in its path. A stereo camera setup was built and the performance of the algorithm on local real-life images, captured through the cameras, was observed. The evaluation of the proposed methodologies was carried out using real life out door images obtained from KITTI dataset and images with radiometric variations from Middlebury stereo dataset

Development of a probabilistic perception system for camera-lidar sensor fusion

La estimación de profundidad usando diferentes sensores es uno de los desafíos clave para dotar a las máquinas autónomas de sólidas capacidades de percepción robótica. Ha habido un avance sobresaliente en el desarrollo de técnicas de estimación de profundidad unimodales basadas en cámaras monoculares, debido a su alta resolución o sensores LiDAR, debido a los datos geométricos precisos que proporcionan. Sin embargo, cada uno de ellos presenta inconvenientes inherentes, como la alta sensibilidad a los cambios en las condiciones de iluminación en el caso delas cámaras y la resolución limitada de los sensores LiDAR. La fusión de sensores se puede utilizar para combinar los méritos y compensar las desventajas de estos dos tipos de sensores. Sin embargo, los métodos de fusión actuales funcionan a un alto nivel. Procesan los flujos de datos de los sensores de forma independiente y combinan las estimaciones de alto nivel obtenidas para cada sensor. En este proyecto, abordamos el problema en un nivel bajo, fusionando los flujos de sensores sin procesar, obteniendo así estimaciones de profundidad que son densas y precisas, y pueden usarse como una fuente de datos multimodal unificada para problemas de estimación de nivel superior. Este trabajo propone un modelo de campo aleatorio condicional (CRF) con múltiples potenciales de geometría y apariencia que representa a la perfección el problema de estimar mapas de profundidad densos a partir de datos de cámara y LiDAR. El modelo se puede optimizar de manera eficiente utilizando el algoritmo Conjúgate Gradient Squared (CGS). El método propuesto se evalúa y compara utilizando el conjunto de datos proporcionado por KITTI Datset. Adicionalmente, se evalúa cualitativamente el modelo, usando datos adquiridos por el autor de esté trabajoMulti-modal depth estimation is one of the key challenges for endowing autonomous machines with robust robotic perception capabilities. There has been an outstanding advance in the development of uni-modal depth estimation techniques based on either monocular cameras, because of their rich resolution or LiDAR sensors due to the precise geometric data they provide. However, each of them suffers from some inherent drawbacks like high sensitivity to changes in illumination conditions in the case of cameras and limited resolution for the LiDARs. Sensor fusion can be used to combine the merits and compensate the downsides of these two kinds of sensors. Nevertheless, current fusion methods work at a high level. They processes sensor data streams independently and combine the high level estimates obtained for each sensor. In this thesis, I tackle the problem at a low level, fusing the raw sensor streams, thus obtaining depth estimates which are both dense and precise, and can be used as a unified multi-modal data source for higher level estimation problems. This work proposes a Conditional Random Field (CRF) model with multiple geometry and appearance potentials that seamlessly represents the problem of estimating dense depth maps from camera and LiDAR data. The model can be optimized efficiently using the Conjugate Gradient Squared (CGS) algorithm. The proposed method was evaluated and compared with the state-of-the-art using the commonly used KITTI benchmark dataset. In addition, the model is qualitatively evaluated using data acquired by the author of this work.MaestríaMagíster en Ingeniería de Desarrollo de Producto

Robust multispectral image-based localisation solutions for autonomous systems

With the recent increase of interest in multispectral imaging, new image-based localisation solutions have emerged. However, its application to visual odometry remains overlooked. Most localisation techniques are still being developed with visible cameras only, because the portability they can offer and the wide variety of cameras available. Yet, other modalities have great potentials for navigation purposes. Infrared imaging for example, provides different information about the scene and is already used to enhance visible images. This is especially the case of far-infrared cameras which can produce images at night and see hot objects like other cars, animals or pedestrians. Therefore, the aim of this thesis is to tackle the lack of research in multispectral localisation and to explore new ways of performing visual odometry accurately with visible and thermal images. First, a new calibration pattern made of LED lights is presented in Chapter 3. Emitting both visible and thermal radiations, it can easily be seen by infrared and visible cameras. Due to its peculiar shape, the whole pattern can be moved around the cameras and automatically identified in the different images recorded. Monocular and stereo calibration are then performed to precisely estimate the camera parameters. Then, a multispectral monocular visual odometry algorithm is proposed in Chapter 4. This generic technique is able to operate in infrared and visible modalities, regardless of the nature of the images. Incoming images are processed at a high frame rate based on a 2D-to-2D unscaled motion estimation method. However, specific keyframes are carefully selected to avoid degenerate cases and a bundle adjustment optimisation is performed on a sliding window to refine the initial estimation. The advantage of visible-thermal odometry is shown on a scenario with extreme illumination conditions, where the limitation of each modality is reached. The simultaneous combination of visible and thermal images for visual odometry is also explored. In Chapter 5, two feature matching techniques are presented and tested in a multispectral stereo visual odometry framework. One method matches features between stereo pairs independently while the other estimates unscaled motion first, before matching the features altogether. Even though these techniques require more processing power to overcome the dissimilarities between V multimodal images, they have the benefit of estimating scaled transformations. Finally, the camera pose estimates obtained with multispectral stereo odometry are fused with inertial data to create a robustified localisation solution which is detailed in Chapter 6. The full state of the system is estimated, including position, velocity, orientation and IMU biases. It is shown that multispectral visual odometry can correct drifting IMU measurements effectively. Furthermore, it is demonstrated that such multi-sensors setups can be beneficial in challenging situations where features cannot be extracted or tracked. In that case, inertial data can be integrated to provide a state estimate while visual odometry cannot

Development of a probabilistic perception system for camera-lidar sensor fusion

La estimación de profundidad usando diferentes sensores es uno de los desafíos clave para dotar a las máquinas autónomas de sólidas capacidades de percepción robótica. Ha habido un avance sobresaliente en el desarrollo de técnicas de estimación de profundidad unimodales basadas en cámaras monoculares, debido a su alta resolución o sensores LiDAR, debido a los datos geométricos precisos que proporcionan. Sin embargo, cada uno de ellos presenta inconvenientes inherentes, como la alta sensibilidad a los cambios en las condiciones de iluminación en el caso delas cámaras y la resolución limitada de los sensores LiDAR. La fusión de sensores se puede utilizar para combinar los méritos y compensar las desventajas de estos dos tipos de sensores. Sin embargo, los métodos de fusión actuales funcionan a un alto nivel. Procesan los flujos de datos de los sensores de forma independiente y combinan las estimaciones de alto nivel obtenidas para cada sensor. En este proyecto, abordamos el problema en un nivel bajo, fusionando los flujos de sensores sin procesar, obteniendo así estimaciones de profundidad que son densas y precisas, y pueden usarse como una fuente de datos multimodal unificada para problemas de estimación de nivel superior. Este trabajo propone un modelo de campo aleatorio condicional (CRF) con múltiples potenciales de geometría y apariencia que representa a la perfección el problema de estimar mapas de profundidad densos a partir de datos de cámara y LiDAR. El modelo se puede optimizar de manera eficiente utilizando el algoritmo Conjúgate Gradient Squared (CGS). El método propuesto se evalúa y compara utilizando el conjunto de datos proporcionado por KITTI Datset. Adicionalmente, se evalúa cualitativamente el modelo, usando datos adquiridos por el autor de esté trabajoMulti-modal depth estimation is one of the key challenges for endowing autonomous machines with robust robotic perception capabilities. There has been an outstanding advance in the development of uni-modal depth estimation techniques based on either monocular cameras, because of their rich resolution or LiDAR sensors due to the precise geometric data they provide. However, each of them suffers from some inherent drawbacks like high sensitivity to changes in illumination conditions in the case of cameras and limited resolution for the LiDARs. Sensor fusion can be used to combine the merits and compensate the downsides of these two kinds of sensors. Nevertheless, current fusion methods work at a high level. They processes sensor data streams independently and combine the high level estimates obtained for each sensor. In this thesis, I tackle the problem at a low level, fusing the raw sensor streams, thus obtaining depth estimates which are both dense and precise, and can be used as a unified multi-modal data source for higher level estimation problems. This work proposes a Conditional Random Field (CRF) model with multiple geometry and appearance potentials that seamlessly represents the problem of estimating dense depth maps from camera and LiDAR data. The model can be optimized efficiently using the Conjugate Gradient Squared (CGS) algorithm. The proposed method was evaluated and compared with the state-of-the-art using the commonly used KITTI benchmark dataset. In addition, the model is qualitatively evaluated using data acquired by the author of this work.MaestríaMagíster en Ingeniería de Desarrollo de Producto

Cross-source Point Cloud Registration: Challenges, Progress and Prospects

The emerging topic of cross-source point cloud (CSPC) registration has attracted increasing attention with the fast development background of 3D sensor technologies. Different from the conventional same-source point clouds that focus on data from same kind of 3D sensor (e.g., Kinect), CSPCs come from different kinds of 3D sensors (e.g., Kinect and { LiDAR}). CSPC registration generalizes the requirement of data acquisition from same-source to different sources, which leads to generalized applications and combines the advantages of multiple sensors. In this paper, we provide a systematic review on CSPC registration. We first present the characteristics of CSPC, and then summarize the key challenges in this research area, followed by the corresponding research progress consisting of the most recent and representative developments on this topic. Finally, we discuss the important research directions in this vibrant area and explain the role in several application fields.Comment: Accepted by Neurocomputing 202

Orthorectification of helicopter-borne high resolution experimental burn observation from infra red handheld imagers

To pursue the development and validation of coupled fire-atmosphere models, the wildland fire modeling community needs validation data sets with scenarios where fire-induced winds influence fire front behavior, and with high temporal and spatial resolution. Helicopter-borne infrared thermal cameras have the potential to monitor landscape-scale wildland fires at a high resolution during experimental burns. To extract valuable information from those observations, three-step image processing is required: (a) Orthorectification to warp raw images on a fixed coordinate system grid, (b) segmentation to delineate the fire front location out of the orthorectified images, and (c) computation of fire behavior metrics such as the rate of spread from the time-evolving fire front location. This work is dedicated to the first orthorectification step, and presents a series of algorithms that are designed to process handheld helicopter-borne thermal images collected during savannah experimental burns. The novelty in the approach lies on its recursive design, which does not require the presence of fixed ground control points, hence relaxing the constraint on field of view coverage and helping the acquisition of high-frequency observations. For four burns ranging from four to eight hectares, long-wave and mid infra red images were collected at 1 and 3 Hz, respectively, and orthorectified at a high spatial resolution (<1 m) with an absolute accuracy estimated to be lower than 4 m. Subsequent computation of fire radiative power is discussed with comparison to concurrent space-borne measurementsPeer ReviewedPostprint (published version

The state-of-the-art progress in cloud detection, identification, and tracking approaches: a systematic review

A cloud is a mass of water vapor floating in the atmosphere. It is visible from the ground and can remain at a variable height for some time. Clouds are very important because their interaction with the rest of the atmosphere has a decisive influence on weather, for instance by sunlight occlusion or by bringing rain. Weather denotes atmosphere behavior and is determinant in several human activities, such as agriculture or energy capture. Therefore, cloud detection is an important process about which several methods have been investigated and published in the literature. The aim of this paper is to review some of such proposals and the papers that have been analyzed and discussed can be, in general, classified into three types. The first one is devoted to the analysis and explanation of clouds and their types, and about existing imaging systems. Regarding cloud detection, dealt with in a second part, diverse methods have been analyzed, i.e., those based on the analysis of satellite images and those based on the analysis of images from cameras located on Earth. The last part is devoted to cloud forecast and tracking. Cloud detection from both systems rely on thresholding techniques and a few machine-learning algorithms. To compute the cloud motion vectors for cloud tracking, correlation-based methods are commonly used. A few machine-learning methods are also available in the literature for cloud tracking, and have been discussed in this paper too