Related Publications

Scientific Journals (peer reviewed articles)

[1] Abbood2017SwarmEvolComput illustration Z. Ali Abbood, J. Lavauzelle, É Lutton, J.-M. Rocchisani, J. Louchet, and F. P. Vidal. Voxelisation in the 3-D Fly Algorithm for PET. Swarm and Evolutionary Computation, ??(??):??-??, ?? 2017.  BibTeX  DOI    .pdf

The Fly Algorithm was initially developed for 3-D robot vision applications. It consists in solving the inverse problem of shape reconstruction from projections by evolving a population of 3-D points in space (the `flies'), using an evolutionary optimisation strategy. Here, in its version dedicated to tomographic reconstruction in medical imaging, the flies are mimicking radioactive photon sources. Evolution is controlled using a fitness function based on the discrepancy of the projections simulated by the flies with the actual pattern received by the sensors. The reconstructed radioactive concentration is derived from the population of flies, i.e. a collection of points in the 3-D Euclidean space, after convergence. `Good' flies were previously binned into voxels. In this paper, we study which flies to include in the final solution and how this information can be sampled to provide more accurate datasets in a reduced computation time. We investigate the use of density fields, based on Metaballs and on Gaussian functions respectively, to obtain a realistic output. The spread of each Gaussian kernel is modulated in function of the corresponding fly fitness. The resulting volumes are compared with previous work in terms of normalised-cross correlation. In our test-cases, data fidelity increases by more than 10% when density fields are used instead of binning. Our method also provides reconstructions comparable to those obtained using well-established techniques used in medicine (filtered back- projection and ordered subset expectation-maximisation).

Keywords: Fly algorithm; Evolutionary computation; tomography reconstruction; iterative algorithms; inverse problems; co-operative co-evolution

[2] Vidal2012IEEETransBiomedEng illustration F. P. Vidal, P.-F. Villard, and É. Lutton. Tuning of patient specific deformable models using an adaptive evolutionary optimization strategy. IEEE Transactions on Biomedical Engineering, 59(10):2942-2949, October 2012.  BibTeX  DOI  PMID  .pdf

We present and analyze the behavior of an evolutionary algorithm designed to estimate the parameters of a complex organ behavior model. The model is adaptable to account for patient's specificities. The aim is to finely tune the model to be accurately adapted to various real patient datasets. It can then be embedded, for example, in high fidelity simulations of the human physiology. We present here an application focused on respiration modeling. The algorithm is automatic and adaptive. A compound fitness function has been designed to take into account for various quantities that have to be minimized. The algorithm efficiency is experimentally analyzed on several real test cases: 1) three patient datasets have been acquired with the "breath hold" protocol, and 2) two datasets corresponds to 4-D CT scans. Its performance is compared with two traditional methods (downhill simplex and conjugate gradient descent): a random search and a basic real-valued genetic algorithm. The results show that our evolutionary scheme provides more significantly stable and accurate results.

Keywords: Evolutionary computation, inverse problems, medical simulation, adaptive algorithm

International Conferences (peer reviewed articles)

[1] Abbood2017EvoIASP illustration Z. Ali Abbood, O. Amlal, and F. P. Vidal. Evolutionary Art Using the Fly Algorithm. In Applications of Evolutionary Computation, volume 10199 of Lecture Notes in Computer Science, pages 455-470, Amsterdam, The Netherlands, April 2017. Springer, Heidelberg.  BibTeX  DOI  .pdf 

This study is about Evolutionary art such as digital mosaics. The most common techniques to generate a digital mosaic effect heavily rely on Centroidal Voronoi diagrams. Our method generates artistic images as an optimisation problem without the introduction of any a priori knowledge or constraint other than the input image. We adapt a cooperative co-evolution strategy based on the Parisian evolution approach, the Fly algorithm, to produce artistic visual effects from an input image (e.g. a photograph). The primary usage of the Fly algorithm is in computer vision, especially stereo-vision in robotics. It has also been used in image reconstruction for tomography. Until now the individuals correspond to simplistic primitives: Infinitely small 3-D points. In this paper, the individuals have a much more complex representation and represent tiles in a mosaic. They have their own position, size, colour, and rotation angle. We take advantage of graphics processing units (GPUs) to generate the images using the modern OpenGL Shading Language. Different types of tiles are implemented, some with transparency, to generate different visual effects, such as digital mosaic and spray paint. A user study has been conducted to evaluate some of our results. We also compare results with those obtained with GIMP, an open-source software for image manipulation.

Keywords: Digital mosaic; Evolutionary art; Fly algorithm; Parisian evolution; Cooperative co-evolution

[2] Vidal2013MIBISOC-A illustration F. P. Vidal, Y. L. Pavia, J.-M. Rocchisani, J. Louchet, and É. Lutton. Artificial evolution strategy for pet reconstruction. In International Conference on Medical Imaging Using Bio-Inspired and Soft Computing (MIBISOC2013), pages 39-46, Brussels, Belgium, May 2013.  BibTeX  .pdf 

This paper shows new resutls of our artificial evolution algorithm for Positron Emission Tomography (PET) reconstruction. This imaging technique produces datasets corresponding to the concentration of positron emitters within the patient. Fully three-dimensional (3D) tomographic reconstruction requires high computing power and leads to many challenges. Our aim is to produce high quality datasets in a time that is clinically acceptable. Our method is based on a co-evolution strategy called the “Fly algorithm”. Each fly represents a point in space and mimics a positron emitter. Each fly position is progressively optimised using evolutionary computing to closely match the data measured by the imaging system. The performance of each fly is assessed based on its positive or negative contribution to the performance of the whole population. The final population of flies approximates the radioactivity concentration. This approach has shown promising results on numerical phantom models. The size of objects and their relative concentrations can be calculated in two-dimensional (2D) space. In (3D), complex shapes can be reconstructed. In this paper, we demonstrate the ability of the algorithm to fidely reconstruct more anatomically realistic volumes.

Keywords: Evolutionary computation, inverse problems, adaptive algorithm, Nuclear medicine, Positron emission tomography, Reconstruction algorithms

[3] Vidal2013MIBISOC-B illustration F. P. Vidal, P.-F. Villard, and É. Lutton. Automatic tuning of respiratory model for patient-based simulation. In International Conference on Medical Imaging Using Bio-Inspired and Soft Computing (MIBISOC2013), pages 225-231, Brussels, Belgium, May 2013.  BibTeX  .pdf 

This paper is an overview of a method recently published in a biomedical journal (IEEE Transactions on Biomedical Engineering, http://tbme.embs.org). The method is based on an optimisation technique called “evolutionary strategy” and it has been designed to estimate the parameters of a complex 15-D respiration model. This model is adaptable to account for patient's specificities. The aim of the optimisation algorithm is to finely tune the model so that it accurately fits real patient datasets. The final results can then be embedded, for example, in high fidelity simulations of the human physiology. Our algorithm is fully automatic and adaptive. A compound fitness function has been designed to take into account for various quantities that have to be minimised (here topological errors of the liver and the diaphragm geometries). The performance our implementation is compared with two traditional methods (downhill simplex and conjugate gradient descent), a random search and a basic real-valued genetic algorithm. It shows that our evolutionary scheme provides results that are significantly more stable and accurate than the other tested methods. The approach is relatively generic and can be easily adapted to other complex parametrisation problems when ground truth data is available.

Keywords: Evolutionary computation, inverse problems, medical simulation, adaptive algorithm

[4] Villard2012MMVR illustration P.-F. Villard, F. P. Vidal, F. Bello, and N. W. John. A method to compute respiration parameters for patient-based simulators. In Proceeding of Medicine Meets Virtual Reality 19 - NextMed (MMVR19), volume 173 of Studies in Health Technology and Informatics, pages 529-533, Newport Beach, California, February 2012. IOS Press. Winner of the best poster award.  BibTeX  PMID  .pdf 

We propose a method to automatically tune a patient-based virtual environment training simulator for abdominal needle insertion. The key attributes to be customized in our framework are the elasticity of soft-tissues and the respiratory model parameters. The estimation is based on two 3D Computed Tomography (CT) scans of the same patient at two different time steps. Results are presented on five patients and show that our new method leads to better results than our previous studies with manually tuned parameters.

[5] Vidal2010PPSN illustration F. P. Vidal, É. Lutton, J. Louchet, and J.-M. Rocchisani. Threshold selection, mitosis and dual mutation in cooperative coevolution: application to medical 3D tomography. In International Conference on Parallel Problem Solving From Nature (PPSN'10), volume 6238 of Lecture Notes in Computer Science, pages 414-423, Krakow, Poland, September 2010. Springer, Heidelberg.  BibTeX  DOI  .pdf

We present and analyse the behaviour of specialised operators designed for cooperative coevolution strategy in the framework of 3D tomographic PET reconstruction. The basis is a simple cooperative co-evolution scheme (the “fly algorithm”), which embeds the searched solution in the whole population, letting each individual be only a part of the solution. An individual, or fly, is a 3D point that emits positrons. Using a cooperative co-evolution scheme to optimize the position of positrons, the population of flies evolves so that the data estimated from flies matches measured data. The final population approximates the radioactivity concentration. In this paper, three operators are proposed, threshold selection, mitosis and dual mutation, and their impact on the algorithm efficiency is experimentally analysed on a controlled test-case. Their extension to other cooperative co-evolution schemes is discussed.

[6] Vidal2010EvoIASP illustration F. P. Vidal, J. Louchet, J.-M. Rocchisani, and É. Lutton. New genetic operators in the Fly algorithm: application to medical PET image reconstruction. In Applications of Evolutionary Computation, volume 6024 of Lecture Notes in Computer Science, pages 292-301, Istanbul, Turkey, April 2010. Springer, Heidelberg. Nominated for best paper award.  BibTeX  DOI  .pdf

This paper presents an evolutionary approach for image reconstruction in positron emission tomography (PET). Our reconstruction method is based on a cooperative coevolution strategy (also called Parisian evolution): the “fly algorithm”. Each fly is a 3D point that mimics a positron emitter. The flies' position is progressively optimised using evolutionary computing to closely match the data measured by the imaging system. The performance of each fly is assessed using a “marginal evaluation” based on the positive or negative contribution of this fly to the performance of the population. Using this property, we propose a “thresholded-selection” method to replace the classical tournament method. A mitosis operator is also proposed. It is triggered to automatically increase the population size when the number of flies with negative fitness becomes too low.

[7] Vidal2009EA illustration F. P. Vidal, D. Lazaro-Ponthus, S. Legoupil, J. Louchet, É. Lutton, and J.-M. Rocchisani. Artificial evolution for 3D PET reconstruction. In Proceedings of the 9th international conference on Artificial Evolution (EA'09), volume 5975 of Lecture Notes in Computer Science, pages 37-48, Strasbourg, France, October 2009. Springer, Heidelberg.  BibTeX  DOI  .pdf

This paper presents a method to take advantage of artificial evolution in positron emission tomography reconstruction. This imaging technique produces datasets that correspond to the concentration of positron emitters through the patient. Fully 3D tomographic reconstruction requires high computing power and leads to many challenges. Our aim is to reduce the computing cost and produce datasets while retaining the required quality. Our method is based on a coevolution strategy (also called Parisian evolution) named “Fly algorithm”. Each fly represents a point of the space and acts as a positron emitter. The final population of flies corresponds to the reconstructed data. Using “marginal evaluation”, the fly's fitness is the positive or negative contribution of this fly to the performance of the population. This is also used to skip the relatively costly step of selection and simplify the evolutionary algorithm.

International Conferences (abstracts)

[1] Vidal2011MedPhys illustration F. P. Vidal, M. Folkerts, N. Freud, and S. Jiang. GPU accelerated DRR computation with scatter. Medical Physics, 38(6):3455-3456, July 2011.  BibTeX  DOI  .pdf

Purpose: We propose a fast software library implemented on graphics processing unit (GPU) to compute digitally reconstructed radiographs (DRRs). It takes into account first order Compton scattering.
Methods: The simulation is based on the evaluation of the Beer‐Lambert law and of the Klein‐Nishina equation. The algorithm is fully determinist and has been fully implemented on GPU to achieve clinically acceptable efficiency. A full resolution simulation is performed for primary radiation. A much lower image resolution is used for Compton scattering as it adds a low frequency pattern over the projection image. Each voxel of the CT dataset is considered as a secondary source. The number of photons that reach each voxel is evaluated. Then, for each secondary source, a projection image is computed and integrated in the final image. The photon energy between each secondary source and each pixel is also computed. An interlaced sampling mode is also proposed to further reduce the computation time without sacrificing numerical accuracy. Finally, the speed and accuracy are assessed.
Results: We show that the computations can be fully implemented on the GPU with an original under‐sampling method to produce clinically acceptable results. For example, a simulation can be achieved in less than 7 seconds whilst the maximum relative error remains below 5% and the average relative error below 1.4%. At full resolution, a speed‐up by factor ∼12X is achieved for the GPU implementation with our interlaced‐mode by comparison with our multi‐threaded CPU implementation using 8 threads in parallel.
Conclusions: DRR calculation with scatter is computationally intensive. The use of GPU can achieve clinically acceptable efficiency. A Compton fluence map can be computed in a few seconds using under‐sampling, whilst keeping numerical inaccuracies relatively low. This work can be used for CBCT reconstruction to reduce scatter artifacts.

[2] Vidal2010MedPhys-A illustration F. P. Vidal, J. Louchet, J.-M. Rocchisani, and É. Lutton. Flies for PET: An artificial evolution strategy for image reconstruction in nuclear medicine. Medical Physics, 37(6):3139, July 2010.  BibTeX  DOI  .pdf

Purpose: We propose an evolutionary approach for image reconstruction in nuclear medicine. Our method is based on a cooperative coevolution strategy (also called Parisian evolution): the “fly algorithm”.
Method and Materials: Each individual, or fly, corresponds to a 3D point that mimics a radioactive emitter, i.e. a stochastic simulation of annihilation events is performed to compute the fly's illumination pattern. For each annihilation, a photon is emitted in a random direction, and a second photon is emitted in the opposite direction. The line between two detected photons is called line of response (LOR). If both photons are detected by the scanner, the fly's illumination pattern is updated. The LORs of every fly are aggregated to form the population total illumination pattern. Using genetic operations to optimize the position of positrons, the population of flies evolves so that the population total pattern matches measured data. The final population of flies approximates the radioactivity concentration.
Results: We have developed numerical phantom models to assess the reconstruction algorithm. To date, no scattering and no tissue attenuation have been considered. Whilst this is not physically correct, it allows us to test and validate our approach in the simplest cases. Preliminary results show the validity of this approach in both 2D and fully‐3D modes. In particular, the size of objects, and their relative concentrations can be retrieved in the 2D mode. In fully‐3D, complex shapes can be reconstructed.
Conclusions: An evolutionary approach for PET reconstruction has been proposed and validated using simple test cases. Further work will therefore include the use of more realistic input data (including random events and scattering), which will finally lead to implement the correction of scattering within our algorithm. A comparison study against ML‐EM and/or OS‐EM methods will also need to be conducted.

International Conferences (other presentations)

[1] AliAbbood2015VCBM illustration Zainab Ali Abbood, Jean-Marie Rocchisani, and Franck P. Vidal. Visualisation of PET data in the Fly Algorithm. In Katja Bühler, Lars Linsen, and Nigel W. John, editors, Eurographics Workshop on Visual Computing for Biology and Medicine, pages 211--212. The Eurographics Association, 2015.  BibTeX  DOI  .pdf 

We use the Fly algorithm, an artificial evolution strategy, to reconstruct positron emission tomography (PET) images. The algorithm iteratively optimises the position of 3D points. It eventually produces a point cloud, which needs to be voxelised to produce volume data that can be used with conventional medical image software. However, resulting voxel data is noisy. In our test case with 6,400 points the normalised cross-correlation (NCC) between the reference and the reconstruction is 85.53%; with 25,600 points it is 93.60%. This paper introduces a more robust 3D voxelisation method based on implicit modelling using metaballs to overcome this limitation. With metaballs, the NCC with 6,400 points increases up to 92.21%; and up to 96.26% with 25,600 points.

[2] Vidal2009MIC illustration F. P. Vidal, J. Louchet, É. Lutton, and J.-M. Rocchisani. PET reconstruction using a cooperative coevolution strategy in LOR space. In IEEE Nuclear Science Symposium Conference Record, pages 3363-3366, Orlando, Florida, October 2009. IEEE.  BibTeX  DOI

This paper presents preliminary results of a novel method that takes advantage of artificial evolution for positron emission tomography (PET) reconstruction. Fully 3D tomographic reconstruction in PET requires high computing power and leads to many challenges. To date, the use of such methods is still restricted due to the heavy computing power needed. Evolutionary algorithms have proven to be efficient optimisation techniques in various domains. However the use of evolutionary computation in tomographic reconstruction has been largely overlooked. We propose a computer-based algorithm for fully 3D reconstruction in PET based on artificial evolution and evaluate its relevance.

Keywords: Positron emission tomography, genetic algorithms, optimization methods

Invited Seminars

[1] É. Lutton, and F. P. Vidal. Tomographic 3D reconstruction using cooperative co-evolution. In Medical Imaging Using Bio-inspired and Soft Computing - Second Technical Course, Parma, Italy, February 2012. European Centre for Soft Computing.

This talk presents an overview of the use a cooperative co-evolution approach (the ‘fly algorithm’) in medical image reconstruction. After a rapid introduction to cooperative/co-evolution optimisation techniques, the canonical ‘fly algorithm’, initially developed for stereo vision, will be presented. Its extention to medical SPECT and PET tomography will then be described, and compared to classical reconstruction on synthetic and real data. We will finally focus on some specific genetic operators, designed to improve efficiency and robustness, for which a statistical analysis has been performed.


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