GReTA - a novel Global and Recursive Tracking Algorithm in three dimensions

Tracking multiple moving targets allows quantitative measure of the dynamic behavior in systems as diverse as animal groups in biology, turbulence in fluid dynamics and crowd and traffic control. In three dimensions, tracking several targets becomes increasingly hard since optical occlusions are very likely, i.e. two featureless targets frequently overlap for several frames. Occlusions are particularly frequent in biological groups such as bird flocks, fish schools, and insect swarms, a fact that has severely limited collective animal behavior field studies in the past. This paper presents a 3D tracking method that is robust in the case of severe occlusions. To ensure robustness, we adopt a global optimization approach that works on all objects and frames at once. To achieve practicality and scalability, we employ a divide and conquer formulation, thanks to which the computational complexity of the problem is reduced by orders of magnitude. We tested our algorithm with synthetic data, with experimental data of bird flocks and insect swarms and with public benchmark datasets, and show that our system yields high quality trajectories for hundreds of moving targets with severe overlap. The results obtained on very heterogeneous data show the potential applicability of our method to the most diverse experimental situations.Comment: 13 pages, 6 figures, 3 tables. Version 3 was slightly shortened, and new comprative results on the public datasets (thermal infrared videos of flying bats) by Z. Wu and coworkers (2014) were included. in A. Attanasi et al., "GReTA - A Novel Global and Recursive Tracking Algorithm in Three Dimensions", IEEE Trans. Pattern Anal. Mach. Intell., vol.37 (2015

AGATA, Technical Proposal for an Advanced Gamma Tracking Array for the European Gamma Spectroscopy Community

International audienceAn Advanced GAmma-ray Tracking Array, AGATA, is proposed for high-resolution γ-ray spectroscopy with exotic beams. AGATA will employ highly segmented Ge detectors as well as fully digital electronics and relies on newly developed pulse-shape analysis and tracking methods. The array is being designed in a way that it provides optimal properties for nuclear structure experiments in a wide range of beam velocities (from stopped to v/c ≈ 50%), almost independent of beam quality and background conditions. Selectivity and sensitivity of AGATA will be superior to any existing γ-array by several orders of magnitude. Hence, it will be for a long time a rich source for nuclear structure physics providing the means for new discoveries and opening challenging new perspectives. This document is the initial proposal sent to the European Commission to obtain the necessary funds for the project

High-speed recursive-separable image processing filters

The development of modern technologies in the field of image formation leads to an increase in the size of the generated images, as a result the question of reducing the processing computational costs arises, and this is an important factor in the creation of real-time systems. The study provides a description of high-speed recursive-separable filters for improving the quality of images, which, due to the peculiarities of their implementation, can reduce the number of computational operations required for the image processing process. This type of filters is obtained from two-dimensional linear digital filters, which are modified by applying recursive and separable properties to them. The MATLAB environment computing method for implementation of these filters is described. An extensive performance research of the developed filters has been carried out at various sizes of the test image and on various experimental installations. The comparison with the classical two-dimensional convolution method of the developed filters is demonstrated, and it shows the time gain required for the image processing. The results obtained can be applied in biomedical image processing systems or in vision systems working in heavy weather conditions.The research was carried out at the expense of the Russian Science Foundation grant No. 21-79-10200 at TUSUR

Calibration of multiple cameras for large-scale experiments using a freely moving calibration target

Abstract: Obtaining accurate experimental data from Lagrangian tracking and tomographic velocimetry requires an accurate camera calibration consistent over multiple views. Established calibration procedures are often challenging to implement when the length scale of the measurement volume exceeds that of a typical laboratory experiment. Here, we combine tools developed in computer vision and non-linear camera mappings used in experimental fluid mechanics, to successfully calibrate a four-camera setup that is imaging inside a large tank of dimensions ∼10×25×6m3. The calibration procedure uses a planar checkerboard that is arbitrarily positioned at unknown locations and orientations. The method can be applied to any number of cameras. The parameters of the calibration yields direct estimates of the positions and orientations of the four cameras as well as the focal lengths of the lenses. These parameters are used to assess the quality of the calibration. The calibration allows us to perform accurate and consistent linear ray-tracing, which we use to triangulate and track fish inside the large tank. An open-source implementation of the calibration in Matlab is available. Graphic abstract: [Figure not available: see fulltext.]

Simultaneous measurements of three-dimensional trajectories and wingbeat frequencies of birds in the field

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordData accessibility: We provide data including images recorded by four cameras, camera parameters, videos showing the time variation of the bird 3D positions, and plain text files that include bird id number, positions, times, velocities, accelerations, and wingbeat frequencies at every time step. We also provide the Matlab codes that were used to: (i) detect birds on images; (ii) reconstruct birds' 3D locations using the new stereo-matching algorithm; (iii) track individual's 3D motions; and (iv) calculate wing motion and wingbeat frequency from tracking results. The code and data are available at: https://github.com/linghj/3DTracking.git and https://figshare.com/s/3c572f91b07b06ed30aa.Tracking the movements of birds in three dimensions is integral to a wide range of problems in animal ecology, behaviour and cognition. Multi-camera stereo-imaging has been used to track the three-dimensional (3D) motion of birds in dense flocks, but precise localization of birds remains a challenge due to imaging resolution in the depth direction and optical occlusion. This paper introduces a portable stereo-imaging system with improved accuracy and a simple stereo-matching algorithm that can resolve optical occlusion. This system allows us to decouple body and wing motion, and thus measure not only velocities and accelerations but also wingbeat frequencies along the 3D trajectories of birds. We demonstrate these new methods by analysing six flocking events consisting of 50 to 360 jackdaws (Corvus monedula) and rooks (Corvus frugilegus) as well as 32 jackdaws and 6 rooks flying in isolated pairs or alone. Our method allows us to (i) measure flight speed and wingbeat frequency in different flying modes; (ii) characterize the U-shaped flight performance curve of birds in the wild, showing that wingbeat frequency reaches its minimum at moderate flight speeds; (iii) examine group effects on individual flight performance, showing that birds have a higher wingbeat frequency when flying in a group than when flying alone and when flying in dense regions than when flying in sparse regions; and (iv) provide a potential avenue for automated discrimination of bird species. We argue that the experimental method developed in this paper opens new opportunities for understanding flight kinematics and collective behaviour in natural environments.Human Frontier Science Progra

The Development of Novel Pulse Shape Analysis Algorithms for AGATA

In the field of Nuclear Physics the use of large-scale γ-Ray Tracking (GRT) for arrays like the Advanced Gamma Tracking Array (AGATA) is critical in pushing the envelope of our understanding of the complex phenomena that govern our universe. GRT allows for AGATA to track γ-rays across crystals within the array, allowing for unrivalled Doppler correction and Compton add-back. In order for GRT to function effectively, the interaction position and energy depositions of γ-rays within the array must be effectively determined using Pulse Shape Analysis (PSA). Within AGATA, optimisation-based PSA methods are used to localise γ-ray interactions by comparing experimental detector signals against a simulated basis. A simulated basis has been produced for the A005 AGATA detector crystal, which was used to underpin the development and evaluation of novel PSA methods. Machine Learning was also utilised to perform signal discrimination, compression, correction & regression. Graph-Accelerated k-Nearest Neighbour techniques for PSA were profiled and found to offer significant improvements to execution rate and accuracy. An extensive investigation into the performance of the PSA algorithms with respect to noise level, timeshifting and embedded dimensionality was performed to determine to the most effective algorithm of PSA for AGATA. By utilising the GPU & graph-accelerated algorithm Facebook AI Similarity Search (FAISS) on a principal component analysis reduced 100D embedding, comparable accuracy to the accepted standard was found with an ∼ 43, 000% increase in execution rate. The mathematical framework for the efficient precomputation of the responses of γ-rays that interact multiple times across the crystal (High-Fold) is proposed that should allow the augmentation of Fold-1 kNN search to work on High-Fold with minimal penalty to execution rate. It has also been demonstrated that FAISS can successfully reconstruct a variety of experimental data acquired with AGATA detector crystals

Characterization of Segmented Large Volume, High Purity Germanium Detectors

Gamma ray tracking in future HPGe arrays like AGATA will rely on pulse shape analysis (PSA) of multiple Gamma interactions. For this purpose, a simple and fast procedure was developed which enabled the first full characterization of a segmented large volume HPGe detector. An analytical model for the hole mobility in a Ge crystal lattice was developed to describe the hole drift anisotropy with experimental velocity values along the crystal axis as parameters. The new model is based on the drifted Maxwellian hole distribution in Ge. It is verified by reproducing successfully experimental longitudinal hole anisotropy data. A comparison between electron and hole mobility shows large differences for the longitudinal and tangential velocity anisotropy as a function of the electrical field orientation. Measurements on a 12 fold segmented, n-type, large volume, irregular shaped HPGe detector were performed in order to determine the parameters of anisotropic mobility for electrons and holes as charge carriers created by gamma ray interactions. To characterize the electron mobility the complete outer detector surface was scanned in small steps employing photopeak interactions at 60keV. A precise measurement of the hole drift anisotropy was performed with 356keV rays. The drift velocity anisotropy and crystal geometry cause considerable rise time differences in pulse shapes depending on the position of the spatial charge carrier creation. Pulse shapes of direct and transient signals are reproduced by weighting potential calculations with high precision. The measured angular dependence of rise times is caused by the anisotropic mobility, crystal geometry, changing field strength and space charge effects. Preamplified signals were processed employing digital spectroscopy electronics. Response functions, crosstalk contributions and averaging procedures were taken into account implying novel methods due to the segmentation of the Ge-crystal and the digital electronics. The results are relevant for the future gamma ray tracking detectors where high precision of position information of single gamma ray interactions is required. The high accuracy in simulation enabled very high position resolution using PSA. The first application of this technique in a real experiment aimed at the correction for crystal bending imperfections in a Bragg-spectrometer. A position resolution of 1.4mm (sigma) was achieved with 184keV gamma rays employing the fully characterized detector. By careful characterization of the electronic noise, this result is expected to improve further upon use of optimized filters

Dynamic scaling in natural swarms

Collective behaviour in biological systems presents theoretical challenges beyond the borders of classical statistical physics. The lack of concepts such as scaling and renormalization is particularly problematic, as it forces us to negotiate details whose relevance is often hard to assess. In an attempt to improve this situation, we present here experimental evidence of the emergence of dynamic scaling laws in natural swarms of midges. We find that spatio-temporal correlation functions in different swarms can be rescaled by using a single characteristic time, which grows with the correlation length with a dynamical critical exponent z ≈ 1, a value not found in any other standard statistical model. To check whether out-of-equilibrium effects may be responsible for this anomalous exponent, we run simulations of the simplest model of self-propelled particles and find z ≈ 2, suggesting that natural swarms belong to a novel dynamic universality class. This conclusion is strengthened by experimental evidence of the presence of non-dissipative modes in the relaxation, indicating that previously overlooked inertial effects are needed to describe swarm dynamics. The absence of a purely dissipative regime suggests that natural swarms undergo a near-critical censorship of hydrodynamics. Swarms and statistical physics seem like natural bedfellows, but concepts like scaling are yet to prove directly applicable to insect group dynamics. A study of midges suggests they are, and that they may give rise to a new universality class.Instituto de Física de Líquidos y Sistemas Biológico