Learning to Transform Time Series with a Few Examples

We describe a semi-supervised regression algorithm that learns to transform one time series into another time series given examples of the transformation. This algorithm is applied to tracking, where a time series of observations from sensors is transformed to a time series describing the pose of a target. Instead of defining and implementing such transformations for each tracking task separately, our algorithm learns a memoryless transformation of time series from a few example input-output mappings. The algorithm searches for a smooth function that fits the training examples and, when applied to the input time series, produces a time series that evolves according to assumed dynamics. The learning procedure is fast and lends itself to a closed-form solution. It is closely related to nonlinear system identification and manifold learning techniques. We demonstrate our algorithm on the tasks of tracking RFID tags from signal strength measurements, recovering the pose of rigid objects, deformable bodies, and articulated bodies from video sequences. For these tasks, this algorithm requires significantly fewer examples compared to fully-supervised regression algorithms or semi-supervised learning algorithms that do not take the dynamics of the output time series into account

A software solution for recording circadian oscillator features in time-lapse live cell microscopy

BACKGROUND: Fluorescent and bioluminescent time-lapse microscopy approaches have been successfully used to investigate molecular mechanisms underlying the mammalian circadian oscillator at the single cell level. However, most of the available software and common methods based on intensity-threshold segmentation and frame-to-frame tracking are not applicable in these experiments. This is due to cell movement and dramatic changes in the fluorescent/bioluminescent reporter protein during the circadian cycle, with the lowest expression level very close to the background intensity. At present, the standard approach to analyze data sets obtained from time lapse microscopy is either manual tracking or application of generic image-processing software/dedicated tracking software. To our knowledge, these existing software solutions for manual and automatic tracking have strong limitations in tracking individual cells if their plane shifts. RESULTS: In an attempt to improve existing methodology of time-lapse tracking of a large number of moving cells, we have developed a semi-automatic software package. It extracts the trajectory of the cells by tracking theirs displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level or cell displacement. As an example, we present here single cell circadian pattern and motility analysis of NIH3T3 mouse fibroblasts expressing a fluorescent circadian reporter protein. Using Circadian Gene Express plugin, we performed fast and nonbiased analysis of large fluorescent time lapse microscopy datasets. CONCLUSIONS: Our software solution, Circadian Gene Express (CGE), is easy to use and allows precise and semi-automatic tracking of moving cells over longer period of time. In spite of significant circadian variations in protein expression with extremely low expression levels at the valley phase, CGE allows accurate and efficient recording of large number of cell parameters, including level of reporter protein expression, velocity, direction of movement, and others. CGE proves to be useful for the analysis of widefield fluorescent microscopy datasets, as well as for bioluminescence imaging. Moreover, it might be easily adaptable for confocal image analysis by manually choosing one of the focal planes of each z-stack of the various time points of a time series. AVAILABILITY: CGE is a Java plugin for ImageJ; it is freely available at: http://bigwww.epfl.ch/sage/soft/circadian/

Support Vector Machines in R

Being among the most popular and efficient classification and regression methods currently available, implementations of support vector machines exist in almost every popular programming language. Currently four R packages contain SVM related software. The purpose of this paper is to present and compare these implementations.

Extended Target Tracking and Classification Using Neural Networks

Extended target/object tracking (ETT) problem involves tracking objects which potentially generate multiple measurements at a single sensor scan. State-of-the-art ETT algorithms can efficiently exploit the available information in these measurements such that they can track the dynamic behaviour of objects and learn their shapes simultaneously. Once the shape estimate of an object is formed, it can naturally be utilized by high-level tasks such as classification of the object type. In this work, we propose to use a naively deep neural network, which consists of one input, two hidden and one output layers, to classify dynamic objects regarding their shape estimates. The proposed method shows superior performance in comparison to a Bayesian classifier for simulation experiments

A Laboratory Experiment on Robot Contouring with Force Feedback

In this paper we describe a laboratory experiment which is part of a laboratory orientated robotics class taken by seniors and first year graduate students. This experiment is designed to introduce students to real-time robot control system hardware and software. The experiment attempts to fortify material covered m an introductory (non laboratory orientated) class on robotics. The issues covered by this experiments include: kinematics, dynamics, robot drive mechanisms, interfacing of sensors and force control aspects. Students were also required to learn many aspects of real time programming for control applications. We document this entire experiment so it may be reorganized and repeated. We discuss educational and research value of this experiment

2D mapping of strongly deformable cell nuclei, based on contour matching

The spatiotemporal dynamics of protein complexes and genome loci are functionally linked to cellular health status. To study the inherent motion of subnuclear particles, it is essential to remove any superimposed component stemming from displacement and deformation of the nucleus. In this article, we propose a mapping of the nuclear interior, which is based on the deformation of the nuclear contour and has no shape constraints. This registration procedure enabled an accurate estimation of telomere mobility in living human cells undergoing dramatic nuclear deformations. Given the large variety of pathologies and cellular processes that are associated with strong nuclear shape changes, the contour mapping algorithm has generic value for improving the accuracy of mobility measurements of genome loci and intranuclear macromolecule complexes

Computer analysis of objects’ movement in image sequences: methods and applications

Computer analysis of objects’ movement in image sequences is a very complex problem, considering that it usually involves tasks for automatic detection, matching, tracking, motion analysis and deformation estimation. In spite of its complexity, this computational analysis has a wide range of important applications; for instance, in surveillance systems, clinical analysis of human gait, objects recognition, pose estimation and deformation analysis. Due to the extent of the purposes, several difficulties arise, such as the simultaneous tracking of manifold objects, their possible temporary occlusion or definitive disappearance from the image scene, changes of the viewpoints considered in images acquisition or of the illumination conditions, or even nonrigid deformations that objects may suffer in image sequences. In this paper, we present an overview of several methods that may be considered to analyze objects’ movement; namely, for their segmentation, tracking and matching in images, and for estimation of the deformation involved between images.This paper was partially done in the scope of project “Segmentation, Tracking and Motion Analysis of Deformable (2D/3D) Objects using Physical Principles”, with reference POSC/EEA-SRI/55386/2004, financially supported by FCT -Fundação para a Ciência e a Tecnologia from Portugal. The fourth, fifth and seventh authors would like to thank also the support of their PhD grants from FCT with references SFRH/BD/29012/2006, SFRH/BD/28817/2006 and SFRH/BD/12834/2003, respectively