@article{Gray2018GenetProgramEvolvableMach,
  title = {Data exploration in evolutionary reconstruction of {PET} images},
  journal = {Genetic Programming and Evolvable Machines},
  volume = 19,
  number = 3,
  pages = {391-419},
  year = 2018,
  month = sep,
  issn = {1573-7632},
  doi = {10.1007/s10710-018-9330-7},
  author = {Cameron C. Gray and Shatha F. {Al-Maliki} and Franck P. Vidal},
  keywords = {Fly Algorithm},
  keywords = {Tomography reconstruction},
  keywords = {Information visualisation},
  keywords = {Data exploration},
  keywords = {Artificial evolution},
  keywords = {Parisian evolution},
  abstract = {This work is based on a cooperative co-evolution algorithm called 
    `Fly Algorithm', which is an evolutionary algorithm (EA) where individuals 
    are called `flies'. It is a specific case of the `Parisian Approach' where 
    the solution of an optimisation problem is a set of individuals 
    (e.g. the whole population) instead of a single individual (the best one) as 
    in typical EAs. The optimisation problem considered here is tomography 
    reconstruction in positron emission tomography (PET). It estimates 
    the concentration of a radioactive substance (called a radiotracer) within 
    the body. Tomography, in this context, is considered as a difficult 
    ill-posed inverse problem. The Fly Algorithm aims at optimising 
    the position of 3-D points that mimic the radiotracer. At the end of 
    the optimisation process, the fly population is extracted as it corresponds 
    to an estimate of the radioactive concentration. During the optimisation 
    loop a lot of data is generated by the algorithm, such as image metrics, 
    duration, and internal states. This data is recorded in a log file that 
    can be post-processed and visualised. We propose using information 
    visualisation and user interaction techniques to explore the algorithm's 
    internal data. Our aim is to better understand what happens during 
    the evolutionary loop. Using an example, we demonstrate that it is possible 
    to interactively discover when an early termination could be triggered. 
    It is implemented in a new stopping criterion. It is tested on two other 
    examples on which it leads to a 60\% reduction of the number of iterations 
    without any loss of accuracy.},
  pdf = {./pdf/Gray2018GenetProgramEvolvableMach.pdf}
}
@article{AliAbbood2017ArtsAndScience,
  title = {{Fly4Arts}: Evolutionary Digital Art with the {Fly} Algorithm},
  journal = {{ISTE} Arts \& Science},
  volume = {17},
  number = 1,
  pages = {11-16},
  year = 2017,
  month = oct,
  issn = {2515-8767},
  doi = {10.21494/ISTE.OP.2017.0177},
  author = {Zainab Ali Abbood and Franck P. Vidal},
  keywords = {Digital mosaic, Evolutionary art, Fly Algorithm, Parisian evolution, Cooperative co-evolution},
  abstract = {The aim of this study is to generate artistic images, such as 
    digital mosaics, as an optimisation problem without the introduction of 
    any a priori knowledge or constraint other than an input image. 
    The usual practice to produce digital mosaic images heavily relies on 
    Centroidal Voronoi diagrams. We demonstrate here that it can be modelled 
    as an optimisation problem solved using a cooperative co-evolution 
    strategy based on the Parisian evolution approach, the Fly algorithm. 
    An individual is called a fly. Its aim of the algorithm is to optimise 
    the position of infinitely small 3-D points (the flies). The Fly 
    algorithm has been initially used in real-time stereo vision for 
    robotics. It has also demonstrated promising results in image 
    reconstruction for tomography. In this new application, a much more 
    complex representation has been study. A fly is a tile. It has its 
    own position, size, colour, and rotation angle. Our method takes 
    advantage of graphics processing units (GPUs) to generate the images 
    using the modern OpenGL Shading Language (GLSL) and Open Computing 
    Language (OpenCL) to compute the difference between the input image and 
    simulated image. Different types of tiles are implemented, some with 
    transparency, to generate different visual effects, such as digital 
    mosaic and spray paint. An online study with 41 participants has been 
    conducted to compare some of our results with those generated using 
    an open-source software for image manipulation. It demonstrates that 
    our method leads to more visually appealing images.},
  pdf = {./pdf/AliAbbood2017ArtsAndScience.pdf}
}

@article{Abbood2017SwarmEvolComput,
  author = "Zainab {Ali Abbood} and Julien Lavauzelle and \'Evelyne Lutton and 
            Jean-Marie Rocchisani and Jean Louchet and Franck P. Vidal",
  title = "Voxelisation in the 3-D Fly Algorithm for PET",
  journal = "Swarm and Evolutionary Computation",
  year = 2017,
  volume = 36,
  pages = "91-105",
  month = oct,
  abstract = "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).",
  doi = "10.1016/j.swevo.2017.04.001",
  issn = "2210-6502",
  keywords = "Fly algorithm; Evolutionary computation; tomography 
    reconstruction; iterative algorithms; inverse problems; 
    co-operative co-evolution",
  publisher = {Elsevier},
  pdf = {pdf/Abbood2017SwarmEvolComput.pdf},
}
@article{Vidal2016ComputMedImagingGraph,
  author = "Franck P. Vidal and Pierre-Fr\'ed\'eric Villard",
  title = "Development and validation of real-time simulation of X-ray imaging 
    with respiratory motion",
  journal = "Computerized Medical Imaging and Graphics",
  year = 2016,
  volume = 49,
  pages = "1-15",
  month = apr,
  abstract = "We present a framework that combines evolutionary 
    optimisation, soft tissue modelling and ray tracing on GPU to 
    simultaneously compute the respiratory motion and X-ray imaging in 
    real-time. Our aim is to provide validated building blocks with high 
    fidelity to closely match both the human physiology and the physics of 
    X-rays. A CPU-based set of algorithms is presented to model organ 
    behaviours during respiration. Soft tissue deformation is computed with an
    extension of the Chain Mail method. Rigid elements move according to 
    kinematic laws. A GPU-based surface rendering method is proposed to 
    compute the X-ray image using the Beer–Lambert law. It is provided as an 
    open-source library. A quantitative validation study is provided to 
    objectively assess the accuracy of both components: (i) the respiration 
    against anatomical data, and (ii) the X-ray against the Beer–Lambert law and 
    the results of Monte Carlo simulations. Our implementation can be used in 
    various applications, such as interactive medical virtual environment to 
    train percutaneous transhepatic cholangiography in interventional radiology,
     2D/3D registration, computation of digitally reconstructed radiograph, 
     simulation of 4D sinograms to test tomography reconstruction tools.",
  doi = "10.1016/j.compmedimag.2015.12.002",
  pmid = {26773644},
  issn = "0895-6111",
  keywords = "X-ray simulation, Deterministic simulation (ray-tracing), 
    Digitally reconstructed radiograph, Respiration simulation, 
    Medical virtual environment, Imaging guidance, 
    Interventional radiology training",
  publisher = {Elsevier},
  pdf = {pdf/Vidal2016ComputMedImagingGraph.pdf},
}
@article{Villard2014IntJComputAssistRadiolSurg,
  author = {P. F. Villard and F. P. Vidal and L. {ap Cenydd} and R. Holbrey and 
    S. Pisharody and S. Johnson and A. Bulpitt and N. W. John and
    F. Bello and D. Gould},
  title = {Interventional radiology virtual simulator for liver biopsy},
  journal = {International Journal of Computer Assisted Radiology and Surgery},
  year = 2014,
  volume = 9,
  pages = {255-267},
  number = 2,
  month = mar,
  abstract = {Purpose: Training in Interventional Radiology currently uses 
    the apprenticeship model, where clinical and technical skills of invasive 
    procedures are learnt during practice in patients. This apprenticeship 
    training method is increasingly limited by regulatory restrictions 
    on working hours, concerns over patient risk through 
    trainees' inexperience and the variable exposure to case mix and 
    emergencies during training. To address this, we have developed 
    a computer-based simulation of visceral needle puncture procedures.
    Methods: A real-time framework has been built that includes:
    segmentation, physically based modelling, haptics rendering, 
    pseudo-ultrasound generation and the concept of a physical mannequin. 
    It is the result of a close collaboration between different universities, 
    involving computer scientists, clinicians, clinical engineers and 
    occupational psychologists.
    Results: The technical implementation of the framework is a robust and 
    real-time simulation environment combining a physical platform and 
    an immersive computerized virtual environment. The face, content and 
    construct validation have been previously assessed, showing 
    the reliability and effectiveness of this framework, as well as 
    its potential for teaching visceral needle puncture.
    Conclusion: A simulator for ultrasound-guided liver biopsy 
    has been developed. It includes functionalities and metrics extracted from 
    cognitive task analysis. This framework can be useful during training, 
    particularly given the known difficulties in gaining significant practice of
    core skills in patients.},
  doi = {10.1109/s11548-013-0929-0},
  pmid = {23881251},
  keywords = {Biomedical computing, Image segmentation, Simulation, Virtual reality},
  publisher = {Springer Berlin Heidelberg},
  pdf = {pdf/Villard2014IntJComputAssistRadiolSurg.pdf},
}
@article{Villard2014IntJComputAssistRadiolSurg,
  author = {P. F. Villard and F. P. Vidal and L. {ap Cenydd} and R. Holbrey and 
    S. Pisharody and S. Johnson and A. Bulpitt and N. W. John and
    F. Bello and D. Gould},
  title = {Interventional radiology virtual simulator for liver biopsy},
  journal = {International Journal of Computer Assisted Radiology and Surgery},
  year = 2014,
  volume = 9,
  pages = {255-267},
  number = 2,
  month = mar,
  abstract = {Purpose: Training in Interventional Radiology currently uses 
    the apprenticeship model, where clinical and technical skills of invasive 
    procedures are learnt during practice in patients. This apprenticeship 
    training method is increasingly limited by regulatory restrictions 
    on working hours, concerns over patient risk through 
    trainees' inexperience and the variable exposure to case mix and 
    emergencies during training. To address this, we have developed 
    a computer-based simulation of visceral needle puncture procedures.
    Methods: A real-time framework has been built that includes:
    segmentation, physically based modelling, haptics rendering, 
    pseudo-ultrasound generation and the concept of a physical mannequin. 
    It is the result of a close collaboration between different universities, 
    involving computer scientists, clinicians, clinical engineers and 
    occupational psychologists.
    Results: The technical implementation of the framework is a robust and 
    real-time simulation environment combining a physical platform and 
    an immersive computerized virtual environment. The face, content and 
    construct validation have been previously assessed, showing 
    the reliability and effectiveness of this framework, as well as 
    its potential for teaching visceral needle puncture.
    Conclusion: A simulator for ultrasound-guided liver biopsy 
    has been developed. It includes functionalities and metrics extracted from 
    cognitive task analysis. This framework can be useful during training, 
    particularly given the known difficulties in gaining significant practice of
    core skills in patients.},
  doi = {10.1109/s11548-013-0929-0},
  pmid = {23881251},
  keywords = {Biomedical computing, Image segmentation, Simulation, Virtual reality},
  publisher = {Springer Berlin Heidelberg},
  pdf = {pdf/Villard2014IntJComputAssistRadiolSurg.pdf},
}
@article{Vidal2012IEEETransBiomedEng,
  author = {F. P. Vidal and {P.-F.} Villard and \'E. Lutton},
  title = {Tuning of Patient Specific Deformable Models using an Adaptive Evolutionary Optimization Strategy},
  journal = {IEEE Transactions on Biomedical Engineering},
  year = 2012,
  volume = 59,
  pages = {2942-2949},
  number = 10,
  month = oct,
  abstract = {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 patients 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: 
	i) three patient datasets have been acquired with the breath hold protocol, and 
	ii) two datasets corresponds to 4D CT scans. Its performance is compared with 
	two traditional methods (downhill simplex and conjugate gradient descent), 
	a random search and a basic realvalued genetic algorithm. The results show that 
	our evolutionary scheme provides more significantly stable and accurate results.},
  doi = {10.1109/TBME.2012.2213251},
  pmid = {22907958},
  keywords = {Evolutionary computation, inverse problems, medical simulation, 
	adaptive algorithm},
  publisher = {IEEE},
  pdf = {pdf/Vidal2012IEEETransBiomedEng.pdf}
}
@article{Villard2009IntJComputAssistRadiolSurg,
  author = {{P.-F.} Villard and F. P. Vidal and C. Hunt and F. Bello and N. W.
	John and S. Johnson and D. A. Gould},
  title = {A prototype percutaneous transhepatic cholangiography training simulator with real-time breathing motion},
  journal = {International Journal of Computer Assisted Radiology and Surgery},
  year = 2009,
  volume = 4,
  pages = {571-578},
  number = 6,
  month = nov,
  abstract = {Purpose: We present here a simulator for interventional radiology
	focusing on percutaneous transhepatic cholangiography (PTC). This
	procedure consists of inserting a needle into the biliary tree using
	fluoroscopy for guidance. Methods: The requirements of the simulator
	have been driven by a task analysis. The three main components have
	been identified: the respiration, the real-time X-ray display (fluoroscopy)
	and the haptic rendering (sense of touch). The framework for modelling
	the respiratory motion is based on kinematics laws and on the Chainmail
	algorithm. The fluoroscopic simulation is performed on the graphic
	card and makes use of the Beer-Lambert law to compute the X-ray attenuation.
	Finally, the haptic rendering is integrated to the virtual environment
	and takes into account the soft-tissue reaction force feedback and
	maintenance of the initial direction of the needle during the insertion.
	Results: Five training scenarios have been created using patient-specific
	data. Each of these provides the user with variable breathing behaviour,
	fluoroscopic display tuneable to any device parameters and needle
	force feedback. Conclusions A detailed task analysis has been used
	to design and build the PTC simulator described in this paper. The
	simulator includes real-time respiratory motion with two independent
	parameters (rib kinematics and diaphragm action), on-line fluoroscopy
	implemented on the Graphics Processing Unit and haptic feedback to
	feel the soft-tissue behaviour of the organs during the needle insertion.},
  doi = {10.1007/s11548-009-0367-1},
  pmid = {20033333},
  keywords = {Interventional radiology; Virtual environments; Respiration simulation;
	X-ray simulation; Needle puncture; Haptics; Task analysis},
  publisher = {Springer},
  pdf = {pdf/Villard2009IntJComputAssistRadiolSurg.pdf}
}
@article{Vidal2008ComputAnimatVirtW,
  author = {F. P. Vidal and N. W. John and D. A. Gould and A. E. Healey},
  title = {Simulation of Ultrasound Guided Needle Puncture using Patient Specific
	Data with {3D} Textures and Volume Haptics},
  journal = {Computer Animation and Virtual Worlds},
  year = 2008,
  volume = 19,
  pages = {111-127},
  number = 2,
  month = may,
  abstract = {We present an integrated system for training ultrasound (US) guided
	needle puncture. Our aim is to provide a validated training tool
	for interventional radiology (IR) that uses actual patient data.
	IR procedures are highly reliant on the sense of touch and so haptic
	hardware is an important part of our solution. A hybrid surface/volume
	haptic rendering of an US transducer is proposed to constrain the
	device to remain outside the bony structures when scanning the patient's
	skin. A volume haptic model is proposed that implements an effective
	model of needle puncture. Force measurements have been made on real
	tissue and the resulting data is incorporated into the model. The
	other input data required is a computed tomography (CT) scan of the
	patient that is used to create the patient specific models. It is
	also the data source for a novel simulation of a virtual US scanner,
	which is used to guide the needle to the correct location.},
  doi = {10.1002/cav.217},
  keywords = {medical virtual environment; imaging guidance; interventional radiology
	training; needle puncture; volume haptics; vertex and pixel shaders},
  publisher = {John Wiley \& Sons},
  pdf = {pdf/Vidal2008ComputAnimatVirtW.pdf}
}
@article{Vidal2006ComputGraphForum,
  author = {F. P. Vidal and F. Bello and K. W. Brodlie and D. A. Gould and N.
	W. John and R. Phillips and N. J. Avis},
  title = {Principles and Applications of Computer Graphics in Medicine},
  journal = {Computer Graphics Forum},
  year = 2006,
  volume = 25,
  pages = {113-137},
  number = 1,
  month = mar,
  abstract = {The medical domain provides excellent opportunities for the application
	of computer graphics, visualization and virtual environments, with
	the potential to help improve healthcare and bring benefits to patients.
	This survey paper provides a comprehensive overview of the state-of-the-art
	in this exciting field. It has been written from the perspective
	of both computer scientists and practising clinicians and documents
	past and current successes together with the challenges that lie
	ahead. The article begins with a description of the software algorithms
	and techniques that allow visualization of and interaction with medical
	data. Example applications from research projects and commercially
	available products are listed, including educational tools; diagnostic
	aids; virtual endoscopy; planning aids; guidance aids; skills training;
	computer augmented reality and use of high performance computing.
	The final section of the paper summarizes the current issues and
	looks ahead to future developments.},
  doi = {10.1111/j.1467-8659.2006.00822.x},
  keywords = {visualization; augmented and virtual realities; computer graphics;
	health; physically-based modeling; medical sciences; simulation},
  publisher = {Blackwell},
  pdf = {pdf/Vidal2006ComputGraphForum.pdf}
}
@article{Vidal2005NuclInstrumMethB,
  author = {F. P. Vidal and J. M. L\'etang and G. Peix and P. Cl{\oe}tens},
  title = {Investigation of artefact sources in synchrotron microtomography
	via virtual X-ray imaging},
  journal = {Nuclear Instruments and Methods in Physics Research B},
  year = 2005,
  volume = 234,
  pages = {333-348},
  number = 3,
  month = jun,
  abstract = {Qualitative and quantitative use of volumes reconstructed by computed
	tomography (CT) can be compromised due to artefacts which corrupt
	the data. This article illustrates a method based on virtual X-ray
	imaging to investigate sources of artefacts which occur in microtomography
	using synchrotron radiation. In this phenomenological study, different
	computer simulation methods based on physical X-ray properties, eventually
	coupled with experimental data, are used in order to compare artefacts
	obtained theoretically to those present in a volume acquired experimentally,
	or to predict them for a particular experimental setup. The article
	begins with the presentation of a synchrotron microtomographic slice
	of a reinforced fibre composite acquired at the European Synchrotron
	Radiation Facility (ESRF) containing streak artefacts. This experimental
	context is used as the motive throughout the paper to illustrate
	the investigation of some artefact sources. First, the contribution
	of direct radiation is compared to the contribution of secondary
	radiations. Then, the effect of some methodological aspects are detailed,
	including under-sampling, sample and camera misalignment, sample
	extending outside of the field of view and photonic noise. The effect
	of harmonic components present in the experimental spectrum are also
	simulated. Afterwards, detector properties, such as its impulse response
	or defective pixels, are taken into account. Finally, the importance
	of phase contrast effects is evaluated. In the last section, this
	investigation is discussed by putting emphasis on the experimental
	context which is used throughout this paper.},
  doi = {10.1016/j.nimb.2005.02.003},
  keywords = {X-ray microtomography; Artefact; Deterministic simulation (ray-tracing);
	Monte Carlo method; Phase contrast; Modulation transfer function},
  publisher = {Elsevier},
  pdf = {pdf/Vidal2005NuclInstrumMethB.pdf}
}

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