short course program

Whether you want to update your skills, boost your career, delve into a new field, or just refresh your memory, the IEEE short courses can help. Learn from experts in your field who have both theoretical knowledge and real-world practical experience. Courses are available in a wide range of topics for professionals in the nuclear science and medical imaging fields. All courses are one or two days in length. Coffee and pastries will be available for participants of the short courses. Lunch, refreshments, lecture notes and a certification of completion are also provided as part of the course registration fee.

Dates: 29 October - 1 November 2016

Silvia Dalla Torre
Short Course Co-Chair
INFN-Sezione di Trieste - Italy

Youngho Seo
Short Course Co-Chair
University of California, San Francisco - USA

organiser: Fabrizio Murtas, CERN and Istituto Nazionale di Fisica Nucleare, Italy

course description

This course provides an overall review of the basic principles that underlie the neutron detection and the possible use of the detectors in fundamental and applied physics. The course is divided in 4 parts starting with the review of the major detectors used up to now. It is followed by the review of the main worldwide neutron facility and the description of future Neutron Spallation Sources. One of the main issues for neutron detection is the simulation of the processes inside the sensitive areas. The characteristics and the performances of the three state-of-the-art software packages (FLUKA, MCNP, GEANT4) will be described. Finally the use of new technologies like Micro Pattern Gas Detectors and new converters will be analysed trying to overcome the worldwide shortage of helium-3. The level of presentation is best suited to those with some prior background in radiation measurements and particle detection, but can also serve to introduce topics that may be outside their experience base. A complete set of course notes are provided to registrants.

course outline

  1. Detection of neutrons
    This course covers the basic principles of neutron detection and gives an overview about the standard techniques for the determination of neutron energy distributions. Due to the fact that neutrons don't carry electric charge, they can be detected instantaneously only by observing charged particles or gamma radiation emitted in neutron-induced nuclear reactions. For this reasons neutron detectors are based on a large variety of construction principles. The course will offer a general description of the detection techniques, from the thermal, slow and intermediate energy range (i.e. below 1 MeV), where only exothermic reactions such >as 10B(n,alpha)7Li, 6Li(n,t)4He, 3He(n,p)3H or 235U(n,f) can be used, up to fast and relativistic neutrons. In this energy range the elastic neutron-proton scattering with the detection of the recoil proton is the most fundamental detection process with a large variety of detectors, from organic scintillators and gas proportional counters to the fission ionization chambers and recoil proton telescopes. The most powerful method for measuring the neutron energy distribution is the time-of-flight technique, which requires a pulsed neutron source. If a pulsed neutron source is not available,the neutron energy distribution must be inferred from the energy-dependence of the detector signal. This technique, usually termed ‘spectrometry’, can even be applied using a small set of integral detectors with significantly different energy-dependent response. Examples are activation foils or Bonner sphere spectrometer. Since neutrons are almost always accompanied by other types of radiation, neutron detectors are usually sensitive to other kinds of radiation. Hence, the capability to discriminate neutron-induced events from events induced by other particles is an essential feature of neutron detectors. Several techniques based on the analysis of signal waveforms using either analogue of digital signal processing will be discussed.
  2. Neutron Facilities
    This course covers the array of neutron facilities available. This is presently very topical; in the coming decade, many older sources are losing, whilst powerful new research facilities are being built or planned. An overview of potential neutron sources is given, with an emphasis on reactor and spallation sources. The background to neutron scattering is given, with some of the common interrogative methods and their subsequent requirements. How the detector performance specifications derive from these requirements is shown. Some of the techniques used, relevant to detector characterisation, testing and development are outlined. Finally, some tips on how to gain access to beam time at neutron user facilities is given.
  3. Neutron Monte Carlo simulation: an overview on FLUKA, MCNP and GEANT4
    The Monte Carlo description of neutron production, interactions and transport is a key aspect of any evaluation of a neutron radiation field, both for dosimetric purposes and for the evaluation of the fluence rate on neutron detectors. In addition, the detector response simulation is an essential ingredient of any measurement. An evaluation of the radiation damage to the detector components is also an issue. Going from radiation shielding purposes to the measurements of physical processes involving neutrons, including the characterization of the detector response, each problem requires peculiar capabilities to radiation transport software. This course presents a review of the treatment of neutrons in three state-of-the-art Monte Carlo codes: FLUKA, MCNP and GEANT4. A special attention will be put on the low-energy regime (below around 20 MeV), where the use of point-wise cross sections is a key issue for advanced analyses. Examples of performances and applications in different problems from fundamental to applied physics, and in a very wide energy range - from the thermal region up to the hundreds MeV/ GeV regime in ADS systems and high energy neutron sources - will be given.
  4. Micro Pattern Gas Detector for neutron detection
    The Micro Pattern Gas Detectors extend the capabilities of the Multi-Wire Proportional Chambers, even them largely used by the High Energy Physics and neutron scattering communities. Very good position resolution, high particle flux capability, radiation tolerance, low material budget, large surfaces and low energy threshold are the key features which make MPGD flexible and widespread devices in High Energy Physics experiments. These features make them interesting solutions also for the next generation neutron scattering instruments and beam monitors. The development of non-standard neutron detectors, possibly based on MPGDs, is important not only because of the 3He shortage, which forces to find urgently valuable alternatives, but also to extend the capabilities of the actual detectors (e.g. very high particle flux capabilities).


Ralf Nolte is head of the working group ‘Neutron Metrology’ at the Physikalisch-Technische Bundesanstalt (PTB), the national metrology institute of Germany. He received a PhD in experimental nuclear physics and has almost thirty years of research experience in nuclear and plasma physics, radiation physics and nuclear data measurements. His present work is related to neutron measurements in the energy range from a few keV to about 200 MeV for various applications, ranging from the characterization of neutron detectors and detector materials to nuclear data work, with the focus on achieving small uncertainties.

Richard Hall Wilton, since 2011, is Detector Group Leader and deputy Division Head of Instrument Technologies at the European Spallation Source (ESS) in Lund, Sweden, with the task of developing and providing the neutron detectors for over 20 instruments at the new green-field facility, as well as finding replacements to the isotope Helium-3 as the detection medium for neutrons. Throughout his career, Richard Hall-Wilton has been involved in the creation process of advanced detector systems, in particular with gaseous detectors and semiconductor detectors. He is an expert in neutron and diamond detector technologies.

Anna Ferrari is a staff physicist at the Helmholtz-Zentrum Dresden-Rossendorf. Ph.D. in particle physics, she developed in the last decade a solid experience in radiation transport Monte Carlo codes. She was leading the simulation work to describe the neutron response in advanced detectors, both for fundamental physics and for diagnostics in fusion reactors. In the last years she has been responsible of the Monte Carlo characterization of the radiation fields in many European projects, going from neutronics studies in accelerator driven systems to the challenging projects dedicated to the particle acceleration from laser-plasma interaction.

Fabrizio Murtas is a Senior Staff Researcher at Laboratori Nazionali di Frascati INFN and Scientific Associate at CERN. After a first period dedicated to the ALEPH experiment at CERN working on the hadron calorimeter and tau physics, he was responsible for the Calorimeter construction of the KLOE CP violation experiment in Frascati. In 2002 he proposed the construction of the triple GEM muon chambers in the small angle area of LHCb experiment at CERN. Recently developed different detectors based on GEM technology used on neutron, burning plasma physics and beam monitoring for cancer treatment. He is an expert in Micro Pattern Gas Detector for neutron detection.

organiser: Paul O’Connor, BNL, USA

course description

This one-day course is intended to introduce physicists and detector specialists to the fundamentals of integrated circuit front end design. The class begins with a discussion of low-noise signal processing and semiconductor devices and then delves into the details of implementing practical circuits in modern CMOS technology. A basic knowledge of detectors and electronics is assumed.

course outline

  1. Pulse Processing Fundamentals
    • Signal formation in detectors
    • Noise and gain mechanisms
    • Pulse processing for amplitude and timing extraction
  2. Semiconductor Technology for Integrated Circuit Front Ends
    • Operation and characteristics of MOS and bipolar transistors
    • Sub-micron CMOS and BICMOS technology
    • Feature size scaling
    • Radiation effects and reliability
    • Mixed-signal circuits
  3. Design methodology and CAD tools; foundry access for research-scale projects
    • Modern VLSI CAD tools
    • Analog and Mixed Signal Design Workflows
    • Physical Design Implementation
    • ASIC technology support and foundry services for research-scale projects
  4. Analog circuit design
    • Analog circuit design
    • Elementary amplifier configurations
    • Building blocks for the analog channel: charge-sensitive and pulse-shaping amplifiers, baseline stabilizers, peak detectors, track/hold, multiplexers, output stages
    • Analog-to-digital and time-to-digital converters (ADC and TDC)
  5. Application examples


Paul O’Connor is associate Head of the Instrumentation Division at Brookhaven National Laboratory. After receiving the Ph.D. degree in solid-state physics from Brown University he worked from 1980-1990 at AT&T Bell Laboratories prior to joining BNL. His research interests are in the field of instrumentation systems for radiation detection, particularly those involving low noise front-end electronics. He is author and co-author of about 110 publications and has been an IEEE member since 1980.

Christophe De La Taille is Director of OMEGA microelectronics lab at Ecole Polytechnique and CNRS/IN2P3 (France). After receiving engineering and Ph.D. degree from Ecole Polytechnique, he joined LAL Orsay and worked on the readout of the ATLAS calorimeter at CERN/LHC and other high energy physics experiments. He was subsequently CTO of IN2P3and recently founded a design lab at Ecole Polytechnique. He is now coordinator of CMS HGCAL electronics. His research interests are in the field of detectors and mixed signal ASIC design. He is author and co-author of about 168 publications and has been an IEEE member since 2003.

Sergio Rescia is a scientist at the Instrumentation Division at Brookhaven National Laboratory. He received an engineering degree from University of Pavia, Italy and a Ph.D. degree from University of Pennsylvania, Philadephia, USA. After joining Brookhaven National Laboratory he has worked on the readout of liquid argon calorimeters (Helios-NA48, Atlas), silicon detectors, time projection chambers (MicroBoone, SBND, Dune, nEXO) and medical electronics. His research interests center in the field of instrumentation for particle and radiation detectors, particularly optimizing the detector - low noise front end interface. He is author or co-author of over 130 publications and has been an IEEE member since 2002.

Kostas C. Kloukinas is a senior electronics engineer at the microelectronics group of the European Research Center for Particle Physics (CERN), Geneva, Switzerland. He received the B.Sc. and Ph.D. degrees from the Physics Department of the University of Ioannina, Greece, in 1991 and 1997, respectively. Since 1993, he has been with the microelectronics group at CERN, working in the field of VLSI circuits and systems for the readout of particle physics detectors and in the development of a radiation-tolerant standard cell libraries and mixed-signal design kits. He is the coordinator of technology support and foundry access services offered by CERN to collaborating High Energy Physics Institutes and Universities. He is author and co-author of about 65 publications and has been an IEEE member since 1997.

organiser: Samo Korpar, University of Maribor and JSI, Slovenia

course description

Photodetectors are important building blocks for many applications in particle physics, medical imaging and homeland security. This one-day course will cover advanced photodetectors most commonly used in these fields. We will begin with the basics of photo detection followed by a quick review of typical applications to illustrate required properties of photodetectors. We will continue with the description of general characteristics of photodetectors including sensitivity (QE, PDE), linearity, excess noise factor (ENF), and timing. After this introductory part we will discuss in detail different vacuum (PMT, MA-PMT, MCP-PMT), solid state (PD, APD, SiPM) and hybrid photodetectors (HPD, HAPD), and briefly review the status of gaseous photodetectors. For each detector type, internal processes from photon conversion to signal formation and their influence on detector characteristics will be discussed, including various methods for characterization and calibration. Typical applications of these detectors will be reviewed with an emphasis on recent advances and limitations which result from the photodetector characteristics. The course will provide an overview of available photodetectors and understanding of their properties, advantages and limitations which is necessary for proper selection and operation of a photodetector for a particular application.

course outline

  1. Basic principles of photo detection and characteristics of photodetectors (S. Korpar, G. Collazuol)
    • Light detection by solid state, vacuum based and gaseous detectors (photoconductive effect and photoelectric effect); photosensitive materials and different types of photocathodes; photodetector window materials (reflection and transmission)s
    • Quick review of typical applications and their requirements (Calorimeters, PET scanners, Cherenkov detectors), light sources for photodetector characterization and calibration
    • General characteristics of photodetectors: quantum efficiency (QE), photo detection efficiency (PDE), linearity of response, signal fluctuations (ENF - excess noise factor), time response (TTS – transit time spread), rate capability and aging, dark counts and after-pulsing, thermal stability, operation in magnetic field, radiation tolerance
  2. Solid state photodetectors (G. Collazuol)
    • Optical properties of silicon, quantum efficiency of silicon photodetectors
    • Photo diode (PD), p-n and p-i-n structures, light detection by photo diode, typical applications.
    • Avalanche photodiode (APD), internal structure of APD, impact ionization rates of electrons and holes, amplification and excess noise factor, thermal stability, p on n and n on p differences, typical applications
    • Silicon photomultiplier (SiPM), Geiger-mode operation of APD, active and passive quenching, typical SiPM internal structure, break-down voltage and gain, output signal, thermal stability, dark noise, after-pulsing, optical cross-talk (internal, external), signal linearity and saturation, excess noise factor, timing properties, photon detection efficiency, p on n and n on p difference, radiation tolerance, other SiPM types (digital SiPM, bulk integrated quench resistor, Silicon Carbide based …), typical applications
  3. Vacuum based photodetectors (S. Korpar)
    • Photomultiplier tube (PMT), photon detection efficiency, different dynode structures, secondary emission coefficient and gain, excess noise factor, voltage divider and optimisation, multi-anode photomultiplier (MA-PMT), position sensitivity and cross talk, timing properties, magnetic field operation, typical applications, typical applications
    • Microchannel-plate photomultiplier (MCP-PMT), internal structure, photon detection efficiency, gain and excess noise factor, photoelectron backscattering, timing properties, position sensitivity and cross-talk in multi-anode type, magnetic field operation, high rate capability, ion feed-back and aging, typical applications
  4. Hybrid photodetectors (S. Korpar)
    • Hybrid photodetector (HPD), hybrid avalanche photodetector (HAPD), internal structures, photon detection efficiency, gain and excess noise factor, photoelectron back-scattering, timing properties, magnetic field operation, ion feed-back, typical applications
  5. Gaseous photodetectors – quick overview (S. Korpar)
    • Multi-wire proportional counters with photosensitive gas admixture (TEA or TMAE) or CsI photocathode, micro pattern gas detectors with CsI photocathode, sealed gas photodetectors with semi-transparent bialkali photocathode


Gianmaria Collazuol is Assistant Professor of Electronics and Advanced Laboratory at the Department of Physics and Astronomy of the University of Padova. His fields of interest and current activities include experimental subnuclear, neutrino and cosmic-ray physics and the development of innovative detectors and related electronics for experimental studies using gamma rays, neutrons and charged particles. He is an internationally recognized expert in the field of solid state photo-detectors.

Samo Korpar is Associate Professor of Physics at the University of Maribor and senior researcher at the Jozef Stefan Institute, Ljubljana. He is an experimental particle physicist, and is one of the leading experts on ring imaging Cherenkov detectors, with a particular emphasis on single photon detection and the corresponding read-out electronics. He has made important contribution to the understanding of properties of multianode photomultiplier tubes, microchannel plate photomultiplier tubes, hybrid photon detectors and solid state based sensors. He worked on the HERA-B and Belle experiments, and is currently leading the construction of the forward RICH of the Belle II experiment. He is also investigating possible applications of very fast low level light sensors in medical imaging.

organiser: Michael Fiederle, Albert-Ludwigs-University Freiburg, Germany

course description

This 1-day course provides an introduction into the important field of room temperature semiconductor detectors RTSD. The course covers material development, characterization techniques and examples of applications. This lecture gives an overview about the different semiconductor materials, the crystal growth and material properties required for the application of X-, Gamma-rays and Neutron detection. The focus of this presentation is material science and the technological and scientific background.

The course is organized in four different topics:

  • Basics of radiation detection with semiconductor materials
  • Material synthesis/purification and crystal growth semiconductor detector materials
  • Crystal Growth and Characterization of semiconductor detector materials
  • Science and Technology of Semiconductors for Thermal Neutron Detection

The level of presentation is best suited to those with some prior background in radiation detection, but can serve to introduce material science.

A complete set of course notes are provided to registrants.


Arnold Burger is a Professor of Physics and Director of the Materials Science and Applications Group at Fisk University. He received a Ph.D. in Materials Science from the Hebrew University in Jerusalem. He and his collaborators have developed technologies for purification, synthesis, crystal growth and detector fabrication based on novel materials for gamma spectroscopy and thermal neutron detection.

Ernesto Dieguez is a Professor of Physics at the Universidad Autónoma de Madrid, and Head of the Crystal Growth Lab, cgl, from the 80`s ( He has published more than 250 international refereed papers and he has completed the supervision of 15 Doctoral Thesis on the field of Crystal Growth. The CGL has several European and National running projects and scientific collaborations with numerous Research Centres around the world. He has personally the interest to spread the knowledge about Crystal growth fundamentals and applications, and he has given several Erasmus Courses on this field.

Zhong He is a Professor of Nuclear Engineering and Radiological Sciences at University of Michigan. He pioneered depth-sensing coplanar-grid and 3-dimensional position-sensitive readout technologies for large volume wide band-gap semiconductor radiation detectors. He and his group have developed low-noise charge-sensitive application specific integrated circuitries for high performance room-temperature semiconductor gamma and neutron imaging spectrometer systems. His group has also developed advanced gamma and neutron imaging technologies for detecting and characterizing special nuclear materials.

Andrea Zappettini is senior researcher at IMEM-CNR, Parma. He is head of the SIGNAL group and IMEM working in the field of research and development of InP bulk crystals, Nonlinear optical characterization of semiconductors, glasses, and polymers and growth and characterization of CdTe and CdZnTe crystals for x-ray detector applications. He is author of 9 international patents and 179 papers on international journal. He is lecturer at the University of Parma in the field of “Fundamentals of crystal growth technology”.

organiser: Claude Comtat, Frédéric Joliot Hospital Facility, CEA, France

course description

This course will provide an overview of medical image reconstruction methods. For the first time, not only X-ray computed tomography (CT) and emission tomography (PET and SPECT), but also magnetic resonance imaging (MRI) will be covered. Both iterative and non-iterative reconstruction methods will be presented, starting from the basics, and progressing to cover more advanced reconstruction techniques. Several examples and reconstruction demonstrations will be presented. The course will start with the basics of analytical tomographic image reconstruction in two-dimension (2D), with a focus for X-ray CT. Advanced topics in three-dimensional (3D) analytical reconstruction will follow for cone-beam CT and PET. Then, the basics of iterative tomographic image reconstruction will be presented, followed by advanced topics in iterative image reconstruction in PET and CT. The course will end with MRI reconstruction.

Prerequisite knowledge includes basic knowledge of the physics of emission (PET & SPECT) and transmission (X-ray CT) imaging system, statistics, and elementary linear algebra. The MR reconstruction part is intended to scientists who are non-MRI specialists.

Please note that this is a 2-day course, but it has been planned so that each day can be taken independently. You can register for this course for both days (SC5), for the first day only (SC5D1), or for the second day only (SC5D2). See the registration information page for details.

course outline

First Morning

  • Introduction (C. Comtat)
  • Basics of analytic image reconstruction for a 2D setting (E. Sidky)
    • Imaging Model
      • The physics of imaging for 2D CT
      • Parallel- and fan-beam scanning configurations
      • Their relation to the Radon transform
    • Reconstruction (inversion of the model)
      • The Fourier central slice theorem
      • Image reconstruction from 2D parallel-beam projection data
      • Image reconstruction from 2D fan-beam projection data
    • Incomplete data
      • Discrete sampling
      • Limited scanning angular range
      • Limited scanning angular range
    • Data inconsistency
      • Non-ideal physical factors: quantum noise, polychromatic beam spectra, X-ray scatter, etc.
      • The corresponding artifacts in the reconstructed images
      • Exploitation of data redundancy to control image artifacts
  • Advanced topics in 3D analytic image reconstruction in cone-beam CT (E. Sidky)
    • Cone-beam CT data and inversion formulas
      • The 3D Radon and X-ray transform
      • 3D Radon transform inversion
      • Tuy's cone-beam (3D X-ray transform) inversion formula
    • Incomplete data
      • Tuy's condition on the scanning trajectory and circular cone-beam CT
      • Approximate cone-beam CT image reconstruction
      • Helical CT and the long-object problem
    • Advances in helical cone-beam CT image reconstruction
      • Grangeat's relation between the 3D Radon and X-ray transform
      • PI-line and m-line based inversion for cone-beam CT
    • Incomplete data revisited
      • A new perspective on 2D CT - ROI imaging with truncated projections
      • ROI imaging in 3D CT
      • A tiny a priori
    • Ongoing research
      • 3D data consistency conditions
      • Exploitation of these conditions for improved exact cone-beam image reconstruction
      • Image quality metrics
      • Model observers for image reconstruction algorithm development (Ideal observer vs. human observer)
  • Advanced topics in 3D analytic image reconstruction in PET (C. Comtat)
    • Image reconstruction from 3D parallel-beam projection data
    • Incomplete data: the reprojection 3DRP algorithm
    • Rebinning algorithms for 3D PET data: single slice rebinning algorithm (SSRB) and the Fourier rebinning algorithm (FORE)

First Afternoon and Second Morning

  • Basics of iterative image reconstruction (A. Reader, C. Comtat)
    • Data and object parameterization: list-mode data, sinograms, voxels and other spatial basis functions
    • Data modelling: system matrix, resolution modeling, data corrections and factorization, model estimation (analytical - Monte Carlo – measured), noise (Poisson – Gaussian)
    • Objective functions: maximum likelihood, least squares, maximum a posteriori
    • Optimization algorithms: ML-EM, OSL, surrogate, gradient-based methods, subsets, convergence
  • Advanced topics in iterative image reconstruction for PET (A. Reader and C. Comtat)
    • Nested EM for linear or non-linear parameter estimation from tomographic data, used for 4D and direct parametric image reconstruction
    • Anatomy-based image priors
    • Mitigation of Gibbs artefacts (PSF modelling)
    • Bias and negative values: NEG, AML
    • Synergistic joint PET-MR reconstruction
  • Advanced topics in iterative image reconstruction for CT (E. Sidky)
    (Background material will be covered quickly with a CT focus)
    • Implicit solution of an imaging model
      • Inversion of complex physical models
      • Image reconstruction from discretely sampled data
      • A different perspective on the classical incomplete data sampling problems
      • The trade-off between image representation and data fidelity
    • Basic principles of iterative image reconstruction (IIR)
      • Algebraic approach
      • Likelihood maximization
      • Exploitation of image sparsity
      • Incorporation of prior knowledge
    • Optimization for IIR in CT
      • Types of optimization problems: convex/non-convex, unconstrained/constrained, smooth/non-smooth
      • Standard solvers used for CT IIR
      • Recent developments in solvers
      • Early stopping and algorithm acceleration
    • Ongoing research
      • A utility-driven approach to IIR algorithm development
      • The search for meaningful IIR algorithm parameterization
      • Integrated IIR algorithm/tomographic system development

Second Afternoon

  • MRI reconstruction (P. Ciuciu)
    This course is intended to scientists who are non-MRI specialists but rather familiar with inverse problem solving in medical imaging (e.g. in PET or CT imaging). For this reason, the background on MR image acquisition/formation will be reviewed before focusing on image reconstruction. In particular, P. Ciuciu will explain how the data are collected in the Fourier (or k-space) along (piecewise) continuous or more regular trajectories in 2D or 3D will be explained. Next, he will provide an overview of the classical ways to perform MR image reconstruction for Cartesian and non-Cartesian acquisition scenarios and he will address how to correct for static field inhomogeneities within the reconstruction process.
    In the following, P. Ciuciu will pay attention to the classical parallel imaging techniques (SENSE, GRAPPA, ...) that are available on the clinical scanners to fasten acquisitions up to a given acceleration factor R. He will outline the main limitations of these approaches that prevent from considering R ≥ 5 in 2D. This will motivate the presentation of compressed sensing (CS) for MRI in the last part of this course. He will briefly review the original CS theory, present the original applications to MRI using conventional acquisition schemes and sparsity-promoting reconstruction algorithms (proximal methods). Finally he will detail recent developments based on his own research that allows one to achieve 40-fold R values at very high resolution. Matlab code with different examples and reconstruction scenarios will be provided as part of the course.
    • Background in MRI: Image formation, contrast
    • Fourier-based approaches for MR image reconstruction
    • Parallel imaging techniques
    • Compressed sensing MRI


Philippe Ciuciu received his PhD in signal processing from the University of Paris-Sud in 2000. After a two-year postdoctoral fellowship in the Life Science Division of the Atomic Energy Commission (CEA), he has been hired by the same institute to develop signal processing methods for functional Magnetic Resonance Imaging (fMRI) data analysis. Since 2007, Dr Ciuciu has joined NeuroSpin, the CEA neuroimaging center dedicated to ultra-high field MRI and its applications to neuroscience. In 2008, he became principal investigator and then was promoted as CEA expert senior scientist for his contributions to biomedical research in the field of signal and image processing for neuroimaging. Dr Ciuciu has conducted an interdisciplinary research with a track record ranging from MRI data acquisition to analysis of functional neuroimaging data (fMRI, MEG). Dr Ciuciu has developed new 3D/3D+time MR image reconstruction algorithms for anatomical and functional MRI data acquired in parallel imaging. Such algorithms have been patented in Japan and Europe. Since 2011, he has collaborated with mathematicians (P. Weiss, J. Kahn) of the IMT institute (Univ. of Toulouse) on compressed sensing (CS) theory and applications to MRI. The main breakthrough achieved during this collaboration was new mathematically-principled and practically feasible CS sampling schemes specifically designed for MRI, which now permit to dramatically accelerate real acquisitions at 7 Tesla by a factor up to 40, a worldwide breakthrough never achieved before.

Claude Comtat is a researcher at the French Atomic Energy Commission (CEA), a government-funded technological research organization. He is with the Frédéric Joliot Hospital Facility (SHFJ) and IMIV, an In Vivo Molecular Imaging multidisciplinary research laboratory. He received his Ph.D. degree in High Energy Physics from the University of Lausanne in 1996. Prior to CEA, he worked as a postdoctoral fellow for two years at the PET Facility of the University of Pittsburgh Medical Center (UPMC) on PET Image Reconstruction with Paul Kinahan and David Townsend. He has coauthored more than 160 research outputs, including 47 peer-reviewed publications. His main research interest is in iterative reconstruction in PET, with an emphasis on data modelling and multi-modality imaging.

Andrew Reader is a Professor of Imaging Sciences at King’s College London (KCL, UK). He was previously a holder of a Canada Research Chair from 2008-2015 at McGill University (Montreal Neurological Institute, Canada) and prior to that was a senior lecturer at the University of Manchester in the UK. Andrew Reader teaches on master’s level courses for medical image reconstruction, and the physics and maths of radionuclide imaging, and has previously been involved with teaching at summer schools in the UK and France. He now has well over 170 research outputs, including 68 peer-reviewed publications. His primary research interest concerns image reconstruction and modelling for positron emission tomography (PET), and more recently its integration with simultaneous magnetic resonance imaging (MRI). Particular topics include joint PET-MR image reconstruction, fully 4D image reconstruction and direct kinetic parameter estimation, particularly applied to imaging of the brain.

Emil Sidky is a Research Associate Professor at the University of Chicago Department of Radiology and Graduate Program for Medical Physics. He received his Ph.D. in physics from The University of Chicago in 1993. He has coauthored approximately 80 publications in the area of his current interests: CT image reconstruction, large-scale optimization, and objective assessment of image quality. He has ongoing research projects in developing image reconstruction algorithms in Digital Breast Tomosynthesis and spectral CT.

organiser: Matthew Kupinski, University of Arizona, USA

course description

This course will cover probability and statistics as applied in a variety of imaging applications. We will start with a review of fundamental material needed for this course including the basic definitions of probability and the many random factors in imaging. We will then cover advanced estimation methods, detector statistics, and statistical image reconstruction at a level that will enable attendees to better understand the state-of-the-art presented in the literature. Special attention will be given to Bayesian estimation and reconstruction methods and comparisons of these methods to non-Bayesian approaches. The very basics of Monte Carlo methods will be presented to introduce the attendees to the terminology. These discussions will culminate in lectures on the statistical nature of image quality and how to define image quality using task performance. ROC analysis and ROC variants will be discussed. Finally, we will end by covering some common pitfalls that arise when computing image quality measures and also discuss the limitations and utility of traditional hypothesis testing methods.

Lectures will include:

  • Review of probability and statistics
  • Common pitfalls in imaging
  • Estimation methods
  • Statistical image reconstruction
  • Detector statistics
  • Basics of Monte Carlo methods
  • Image quality
  • ROC and ROC variants
  • Value and limitations of traditional hypothesis testing

course outline

  • Basic statistics primer (M. Kupinski)
    • Overview of descriptions of random variables and vectors
    • Random objects, images
    • Noise in imaging
  • Estimation methods (L. Furenlid)
    • Maximum-likelihood methods
    • Fisher information
    • Bayesian methods
  • Signal detection (E. Clarkson)
    • ROC analysis
    • Observer models
    • ROC variants
  • Detector statistics and estimation methods (L. Furenlid)
    • Scaled Poisson likelihoods
    • Position and energy estimation
  • Statistical image reconstruction (E. Clarkson)
    • MLEM
    • Bayesian methods
    • Choice of priors (L2 vs L1 norms)
  • Image quality (M. Kupinski)
    • Common pitfalls in medical imaging
    • Tasks, observers, figures of merit
    • Discussion of hypothesis testing


Matthew Kupinski is a Professor at The University of Arizona with appointments in the College of Optical Sciences, the Department of Medical Imaging, and is an affiliate member of the Program in Applied Mathematics. He received a BS degree in physics from Trinity University in San Antonio, Texas in 1995, and received his PhD in 2000 from the University of Chicago. In 2000 he became a post-doctoral researcher under Dr. Harry Barrett at the University of Arizona and became a faculty member in Optical Sciences in 2002. He is the recipient of the 2007 Mark Tetalman Award given out by the Society of Nuclear Medicine and the 2012 recipient of the Graduate and Professional Student Council Outstanding Mentor Award. He is an Associate Editor of the Journal of Medical Imaging, and currently the conference chair for the SPIE Image Perception Conference. He has over 50 peer-reviewed publications, numerous book chapters, and has edited a book. His current and past research funding spans the NIH, corporate projects on Medical Imaging, small-company projects on biometrics, and Department of Energy funding through collaborations with Sandia National Labs and Pacific Northwest National Labs. He has worked in diverse areas of imaging including x-ray, gamma-ray, diffuse optical, magnetic resonance, and neutron imaging.

Lars Furenlid was educated at the University of Arizona and the Georgia Institute of Technology. He is currently a Professor at the University of Arizona and Co-Director of the Center for Gamma-Ray Imaging, with appointments in the Department of Medical Imaging (Radiology) and the College of Optical Sciences. He is also a member of the Graduate Interdisciplinary Degree Program in Biomedical Engineering and the Arizona Cancer Center. Before moving to the University of Arizona, he was a physicist at the National Synchrotron Light Source at Brookhaven National Laboratory. He is a member of the IEEE and the recipient of 2013 IEEE Radiation Instrumentation Outstanding Achievement Award. His major research area is the development and application of detectors, electronics, data-processing algorithms, and systems for biomedical imaging.

Eric Clarkson received his BA in Mathematics, Physics and Philosophy from Rice University, an MS in Physics and a PhD in Mathematics from Arizona State University, and an MS in Optical Sciences from the University of Arizona. He is currently a Professor at the University of Arizona with a joint appointment in Medical Imaging and Optical Sciences, and is also a faculty member in the Applied Mathematics program. He works primarily ni the Center for Gamma Ray Imaging, but also pursues interests in other imaging applications, and in connecting areas of modern mathematics, such as information theory, group theory and operator theory, with image science.

organiser: Patrice Laquerrière, Institut Pluridisciplinaire Hubert Curien, CNRS UMR 7178, France

course description

This course is intended as an introduction to fundamental concepts of biochemistry and molecular biology as they relate to molecular imaging technologies. We will begin with a presentation on the major biomolecules of the cell, including DNA, RNA, and proteins, and how they are generated. We will then consider how these biomolecules come together to form the major subcellular structures, how cells process information through changes in cell signaling, and how this leads to important cellular decisions, such as whether to divide. Some PET and SPECT tracer will be presented to know where they act in a cell and how you can obtain them, chemically speaking. Finally we will present pre-clinical and clinical applications of the main molecules used.

course outline

Introduction: Overview of molecular imaging in biology (P. Laquerrière, Ph. D. applied physic)

Part 1: Biochemistry of the cell (P. Laquerrière)

  • Metabolism
  • DNA synthesis
  • RNA transcription
  • Protein translation
  • Post-translational modification

Part 2: Cellular structure and processes (P. Laquerrière)

  • Subcellular organization of Eukaryotic cells
  • Cell signaling
  • Cell cycle

Part 3: radiochemistry (P. Marchand, Ph.D. radiochemist)

  • Organic chemistry (18-F, 11-C)
  • Complexation chemistry (99m-Tc, 64-Cu, 89-Zr)

Part 4: Applications of molecular imaging to biology (N. Muller, M.D. Nuclear Medicine)

  • Pre-clinical applications
  • Clinical applications


Patrice Laquerrière has worked for more than 10 years at the interface between physic, biology and chemistry. He, first, worked on cryo electron microscopy (cryoEM) to study the effect of biomaterials on cell reaction, in Reims (France). He then moved to NIH (Bethesda, MD, USA) to continue to work on cryoEM in the field of cancer and bone stem cells. He became professor of the University of Strasbourg in 2008. He then works on small animal imaging, still at the interface between physic and biology.

Patrice Marchand was born in France in 1970. After a Master degree in chemistry and radiochemistry he obtained a PhD in organic synthesis at the University of Caen (Normandy). After post-doctoral researches (total synthesis, macromolecular chemistry, PET imaging with 18F derivatives) he joined the research group of Dr. David Brasse in 2011 (IPHC, Strasbourg) as Research Engineer in radiochemistry. His favorite research topics include Amino-Acids, Nucleosides and related compounds labelled with Fluorine-18 for PET imaging.

Nastassja Muller is a MD specialized in Nuclear Medicine. She works as Nuclear Medicine Physician in Haguenau's Hospital (near Strasbourg). She made her medical studies in Strasbourg. She studied medical imaging physics as well. She achieved a Master in "Physique des rayonnements, détecteur, instrumentation et imagerie". She is preparing a PhD in Hubert Curien multidisciplinary Institut (IPHC), working on the use of Nuclear Medicine imaging in hadrontherapy.

short course schedule

date room curie 1 room curie 2 room churchill
Saturday 29 October 2016 SC1 SC2
Sunday 30 October 2016 SC3 SC4
Monday 31 October 2016 SC5 SC6
Tuesday 1 November 2016 SC5 SC7