Breakfast & Science at CIBM
نویسندگان
چکیده
The Centre de Soutien a l'Enseignement of the UNIL (CSE) launched the evaluation of 3 seasons of Breakfast and Science seminars. I will share with you the results of this evaluation and I will present the novelties for the upcoming season. Meritxell Bach is scientific collaborator at the SPC core of the CIBM. 21/11/2014: "Coronary Endothelial Function Assessment Using Self-Gated Cardiac Cine MRI and k-t Sparse SENSE" by Jerome Yerly An introductory talk presenting "The CIBM/CHUV MR" will be given by Roberto Colotti. Time and Place: 10 am at EPFL, CH-F1-614, add to my calendar Abstract: The endothelium plays a major role in maintaining homeostasis and regulating vascular tone by responding to various hormones, neurotransmitters and vasoactive factors. Disruption of this normal vascular function, known as endothelial dysfunction, can lead to pathological inflammatory processes and cardiovascular disease. There is accumulating evidence suggesting that endothelial dysfunction is an early marker for coronary artery disease and can be detected before structural changes of the vessel wall become visible on anatomical images. One approach to discriminate normal from abnormal coronary endothelial function consists of quantifying the coronary vasomotor response to isometric handgrip exercise. Recent studies have demonstrated that bright blood cine MRI is capable of quantifying coronary vasoreactivity non-invasively with excellent reproducibility. However, bright blood cine MRI generally requires ECG triggering, which has several drawbacks: a) the ECG signal is susceptible to RF interference and is not always easily obtained in patients, b) the ECG-gated reconstruction is vulnerable to arrhythmias, and c) the number of cardiac phases is fixed at the time of acquisition. To address these shortcomings, we propose a novel framework that combines golden angle radial data acquisition with compressed sensing and parallel imaging (k-t sparse SENSE) to reconstruct cardiac cine MR images without the need of an external ECG signal. We hypothesize that our proposed framework can accurately assess coronary endothelial function and provide results equivalent to those of the standard ECG-gated approach, while being robust to arrhythmia. Jérôme Yerly is scientific collaborator at the CVMR groupe of CHUV-MRI core of the CIBM. CIBM News and seminars Breakfast & Science at CIBM The endothelium plays a major role in maintaining homeostasis and regulating vascular tone by responding to various hormones, neurotransmitters and vasoactive factors. Disruption of this normal vascular function, known as endothelial dysfunction, can lead to pathological inflammatory processes and cardiovascular disease. There is accumulating evidence suggesting that endothelial dysfunction is an early marker for coronary artery disease and can be detected before structural changes of the vessel wall become visible on anatomical images. One approach to discriminate normal from abnormal coronary endothelial function consists of quantifying the coronary vasomotor response to isometric handgrip exercise. Recent studies have demonstrated that bright blood cine MRI is capable of quantifying coronary vasoreactivity non-invasively with excellent reproducibility. However, bright blood cine MRI generally requires ECG triggering, which has several drawbacks: a) the ECG signal is susceptible to RF interference and is not always easily obtained in patients, b) the ECG-gated reconstruction is vulnerable to arrhythmias, and c) the number of cardiac phases is fixed at the time of acquisition. To address these shortcomings, we propose a novel framework that combines golden angle radial data acquisition with compressed sensing and parallel imaging (k-t sparse SENSE) to reconstruct cardiac cine MR images without the need of an external ECG signal. We hypothesize that our proposed framework can accurately assess coronary endothelial function and provide results equivalent to those of the standard ECG-gated approach, while being robust to arrhythmia. Jérôme Yerly is scientific collaborator at the CVMR groupe of CHUV-MRI core of the CIBM. CIBM News and seminars Breakfast & Science at CIBM 19/08/15 16:04 Breakfast & Science at CIBM Page 2 of 6 http://www.cibm.ch/breakfast_and_science_cibm Figure: Overview of the proposed self-gated framework. (a) Raw data are acquired over multiple cardiac cycles using a free running 2D golden angle radial scheme. (b) A sliding window approach is used to obtain a set of highly undersampled real-time radial data in k-t space. (c) The real-time sub-images are reconstructed using a k-t sparse SENSE model to suppress the undersampling artifacts. (d) From these sub-images, a systolic and diastolic reference frame are selected and used to compute the Pearson correlation coefficient with all the other sub-images from a user selected region of interest around the heart. An in-house arrhythmia detection and rejection algorithm ensures that each systole peak is followed by a diastole peak. (e) The self-gating signal is then derived from the systole correlation signal and used to retrospectively reorder the radial profiles into cardiac phases. (f) Finally, cardiac cine images with high spatial and high temporal resolution are reconstructed. 12/12/2014: "Exploring brain dynamics during resting state" by Giulia Preti An introductory talk presenting the "Signal Processing Core of the CIBM" will be given by Denis Fortun. Time and Place: 10 am at CHUV, add to my calendar Abstract: Functional connectivity based on functional magnetic resonance imaging (fMRI) during resting state is a powerful measure allowing for the observation of brain interactions. By means of this technique, the existence of networks of regions characterised by coherent spontaneous activity in the resting brain has been shown and is nowadays considered a fundamental property of brain functional organization. Recent findings highlighted the non-stationarity of these networks, which is missed by traditional, stationary functional connectivity analysis. This encouraged therefore the development of new methods allowing for the exploration of brain network dynamics. Particularly relevant is the application to brain diseases involving dynamic neuronal processes, like epilepsy. My talk will be focused on new methods to explore dynamic functional connectivity and their potential value in the application to the clinical field. Maria Giulia Preti is scientific collaborator at MRI-SPC core of the CIBM and MIPLAB of EPFL. Functional connectivity based on functional magnetic resonance imaging (fMRI) during resting state is a powerful measure allowing for the observation of brain interactions. By means of this technique, the existence of networks of regions characterised by coherent spontaneous activity in the resting brain has been shown and is nowadays considered a fundamental property of brain functional organization. Recent findings highlighted the non-stationarity of these networks, which is missed by traditional, stationary functional connectivity analysis. This encouraged therefore the development of new methods allowing for the exploration of brain network dynamics. Particularly relevant is the application to brain diseases involving dynamic neuronal processes, like epilepsy. My talk will be focused on new methods to explore dynamic functional connectivity and their potential value in the application to the clinical field. Maria Giulia Preti is scientific collaborator at MRI-SPC core of the CIBM and MIPLAB of EPFL. 06/02/2015: "RF-coil designs for 7 T human brain imaging" by Özlem Ipek 19/08/15 16:04 Breakfast & Science at CIBM Page 3 of 6 http://www.cibm.ch/breakfast_and_science_cibm An introductory talk presenting the "AIT core" will be given by Frédéric Gretsch. Time and Place: 10 am at HUG (Seminar room 2, Radiology, Level P), Geneva, add to my calendar. Abstract: To acquire high-resolution and –sensitivity images at 7 T MR scanner, various hardware solutions can be used: dedicated RF coil design for a certain anatomical region of the human brain, merging high dielectric constant materials with the existing RF coil concepts, use of multi-channel transmit RF coil arrays on a parallel transmit system to steer any signal amplitude or phase. Besides these solutions, safety limitations at 7 T field have been wisely investigated, i.e. simultaneous EEG-fMRI setup at 7 T MR is simulated with finite difference time domain method to assess its RF safety (Figure). My talk will address various RF hardware solutions developed at CIBM for 7 Tesla human brain and extremities proton and multi nuclei imaging and spectroscopy. Özlem Ipek is scientific collaborator at AIT core of the CIBM. To acquire high-resolution and –sensitivity images at 7 T MR scanner, various hardware solutions can be used: dedicated RF coil design for a certain anatomical region of the human brain, merging high dielectric constant materials with the existing RF coil concepts, use of multi-channel transmit RF coil arrays on a parallel transmit system to steer any signal amplitude or phase. Besides these solutions, safety limitations at 7 T field have been wisely investigated, i.e. simultaneous EEG-fMRI setup at 7 T MR is simulated with finite difference time domain method to assess its RF safety (Figure). My talk will address various RF hardware solutions developed at CIBM for 7 Tesla human brain and extremities proton and multi nuclei imaging and spectroscopy. Özlem Ipek is scientific collaborator at AIT core of the CIBM. Figure: a) Geometric model consisting of realistic human head and a set of 64 ring electrodes, safety resistors and leads simulating the EEG cap; the wire branching was designed according to the real cap, terminating in two connectors close to the head; Voxel mesh obtained from the full geometrical model, including the electrolyte gel and (b) head coil array. c) Comparison of measured (left) and simulated (right) B1+ field distributions with and without the EEG cap. The B1+ field distributions are expressed as a fraction of the nominal flip angle. Arrows 1 and 2 indicate more accentuated local variations occurring near the skin, which exhibited stronger differences between measured and simulated maps. The simulations performed on SEMCAD X (Speag, Zurich, Switzerland). (from Ipek et al. ISMRM Safety Workshop 2014, Washington, DC, USA) 27/02/2015: "EEG source imaging" by Anna Custo An introductory talk presenting the "EEG-HUG core" will be given by (to be announced) Time and Place: 10 am at CHUV (auditoire Jequier-Doge), add to my calendar Abstract: Electrical EncephaloGraphy (EEG) is an established technique to measure noninvasively the synchronized activity of large neuron populations. As any imaging technique, EEG comprises a forward and an inverse problem. The forward problem describes the process producing the scalp potentials measured by the EEG cap placed on the subject’s head, whereas the inverse problem explains the reverse process: how measured scalp potentials translate to their generators (i.e., to the neuronal sources). In order to solve the inverse problem (and therefore recover source locations) we need to first build and “invert” the forward process. EEG source imaging is at the heart of a new method developed in our lab (called TESS) that provides source localization for low SNR ongoing brain activity at rest. This is a particularly difficult problem to solve due to the weak set of information we have on resting state activity: we do not know a priori when the brain is in a particular state (spontaneous vs. stimulus‐ evoked activity) and we can not easily separate the signal of interest from the background noise (diffuse sources and low SNR of this kind of signal). TESS uses the specific temporal signature of a brain state to recover its generators via a general linear model estimator. Anna Custo is scientific collaborator at EEG-HUG core of the CIBM. Electrical EncephaloGraphy (EEG) is an established technique to measure noninvasively the synchronized activity of large neuron populations. As any imaging technique, EEG comprises a forward and an inverse problem. The forward problem describes the process producing the scalp potentials measured by the EEG cap placed on the subject’s head, whereas the inverse problem explains the reverse process: how measured scalp potentials translate to their generators (i.e., to the neuronal sources). In order to solve the inverse problem (and therefore recover source locations) we need to first build and “invert” the forward process. EEG source imaging is at the heart of a new method developed in our lab (called TESS) that provides source localization for low SNR ongoing brain activity at rest. This is a particularly difficult problem to solve due to the weak set of information we have on resting state activity: we do not know a priori when the brain is in a particular state (spontaneous vs. stimulus‐ evoked activity) and we can not easily separate the signal of interest from the background noise (diffuse sources and low SNR of this kind of signal). TESS uses the specific temporal signature of a brain state to recover its generators via a general linear model estimator. Anna Custo is scientific collaborator at EEG-HUG core of the CIBM. 19/08/15 16:04 Breakfast & Science at CIBM Page 4 of 6 http://www.cibm.ch/breakfast_and_science_cibm Figure: Diagram describing the workflow of TESS imaging method. 20/03/2015: "Full-field X-ray tomography at TOMCAT" by Anne Bonnin An introductory talk presenting the "Phase contrast and x-ray imaging core" will be given by Anne Bonnin. Time and Place: 10 am at EPFL, CH-F1-614, add to my calendar Abstract: Full-field X-ray tomographic microscopy is a powerful technique to provide non-invasive, quantitative and volumetric investigations on a large range of applications: biology, geology, material characterization, paleontology, etc. During the last decades, improvements have been done worldwide to provide high resolution and also faster acquisition. At synchrotron sources, the specific features of the X-ray radiation are exploited to get high spatial and temporal resolution. In this framework, the beamline for TOmographic Microscopy and Coherent rAdiology experimentTs (TOMCAT) at the Paul Scherrer Institute [1] offers cutting-edge technology and know-how to exploit these peculiarities. Absorption and phase contrast imaging with an isotropic voxel size ranging from 0.16 up to 11 microns are routinely performed in an energy range of 8-45 keV either in whitebeam or monochromatic mode. In this talk, the different phase contrast methods available at the beamline will be illustrated: with simple edge-enhancement, propagation based techniques [2] or grating interferometry [3]. Combined with the in-situ setup (cryo and laser heating system) and/or with ultra-fast acquisitions, it opens the door to new applications in biological and material sciences. In a second part of the talk, more details on the nanoscope will be given. Linking micrometer with nanometer scale, the TOMCAT nanoscope has been commissioned in 2009 [4], providing a theoretical pixel size of about 50 nm and a field of view of 50 microns. Based on the Zernike phase contrast [5], the last improvements on the optical design especially on the beamshaper [6] and the Fresnel Zone Plate -, as well as on the hardware of the setup itself, allow to work from an energy of 8 keV up to 18 keV with a 150 nm resolution (Figure 1). This setup will be illustrated with recent applications in biological (Figure 2) and material sciences. [1] Stampanoni M. et al. (2006) Proc. of SPIE, 6318, U199-U212. [2] Paganin D. et al. (2002), J. Microscopy, 206, 33-40. [3] McDonald S. A et al. (2009), J. Synchrotron Rad., 16, 562572. [4] Stampanoni M. et al. (2009). J. Phys.: Conf. Ser. 186, 012018. [5] Zernike F. (1934). Physica 1, 689. [6] Vartiainen I. et al. (2014). Opt. Lett. 39,1601. Full-field X-ray tomographic microscopy is a powerful technique to provide non-invasive, quantitative and volumetric investigations on a large range of applications: biology, geology, material characterization, paleontology, etc. During the last decades, improvements have been done worldwide to provide high resolution and also faster acquisition. At synchrotron sources, the specific features of the X-ray radiation are exploited to get high spatial and temporal resolution. In this framework, the beamline for TOmographic Microscopy and Coherent rAdiology experimentTs (TOMCAT) at the Paul Scherrer Institute [1] offers cutting-edge technology and know-how to exploit these peculiarities. Absorption and phase contrast imaging with an isotropic voxel size ranging from 0.16 up to 11 microns are routinely performed in an energy range of 8-45 keV either in whitebeam or monochromatic mode. In this talk, the different phase contrast methods available at the beamline will be illustrated: with simple edge-enhancement, propagation based techniques [2] or grating interferometry [3]. Combined with the in-situ setup (cryo and laser heating system) and/or with ultra-fast acquisitions, it opens the door to new applications in biological and material sciences. In a second part of the talk, more details on the nanoscope will be given. Linking micrometer with nanometer scale, the TOMCAT nanoscope has been commissioned in 2009 [4], providing a theoretical pixel size of about 50 nm and a field of view of 50 microns. Based on the Zernike phase contrast [5], the last improvements on the optical design especially on the beamshaper [6] and the Fresnel Zone Plate -, as well as on the hardware of the setup itself, allow to work from an energy of 8 keV up to 18 keV with a 150 nm resolution (Figure 1). This setup will be illustrated with recent applications in biological (Figure 2) and material sciences. [1] Stampanoni M. et al. (2006) Proc. of SPIE, 6318, U199-U212. [2] Paganin D. et al. (2002), J. Microscopy, 206, 33-40. [3] McDonald S. A et al. (2009), J. Synchrotron Rad., 16, 562572. [4] Stampanoni M. et al. (2009). J. Phys.: Conf. Ser. 186, 012018. [5] Zernike F. (1934). Physica 1, 689. [6] Vartiainen I. et al. (2014). Opt. Lett. 39,1601. Figure 1: Siemens star at 16 keV Figure 2: Zernike Phase Contrast radiography of a U-87 MG cell obtained at 8 keV at SLS. Anne Bonnin is scientific collaborator at Phase contrast and x-ray imaging core of the CIBM. 19/08/15 16:04 Breakfast & Science at CIBM Page 5 of 6 http://www.cibm.ch/breakfast_and_science_cibm 17/04/2015: "Superresolution Reconstruction Methodologies for Magnetic Resonance Spectroscopic Imaging" by Jeff Kasten An introductory talk presenting the "MRI-HUG core" will be given by François Lazeyras. Time and Place: 10 am at EPFL, CH-F1-614, add to my calendar Abstract: The ability to procure spatially-localized distributions of biochemical compounds in vivo remains a recurring aspiration within the medical imaging community, carrying the potential to identify certain hallmarks of disease before morphological or behavioral changes are made manifest. Although magnetic resonance spectroscopic imaging (MRSI) portends this aim, it has traditionally been stymied by its inherently low sensitivity, long required acquisition times, and consequent limited spatial resolution. To address these shortcomings, research efforts in MRSI have typically fallen into one of two categories: (1) those that approach the problem from a sequence standpoint, whereby novel accelerated acquisition protocols have been devised in order to push the limits between signal-to-noise and sensitivity, and (2) those inclined towards the development of alternative reconstruction strategies seeking to circumvent the limitations associated with standard inverse Fourier methods. In this talk, I will primarily focus on the latter, recounting the last few decades of research into "superresolution" MRSI reconstruction methods, as well as the current state-of-the-art. The ability to procure spatially-localized distributions of biochemical compounds in vivo remains a recurring aspiration within the medical imaging community, carrying the potential to identify certain hallmarks of disease before morphological or behavioral changes are made manifest. Although magnetic resonance spectroscopic imaging (MRSI) portends this aim, it has traditionally been stymied by its inherently low sensitivity, long required acquisition times, and consequent limited spatial resolution. To address these shortcomings, research efforts in MRSI have typically fallen into one of two categories: (1) those that approach the problem from a sequence standpoint, whereby novel accelerated acquisition protocols have been devised in order to push the limits between signal-to-noise and sensitivity, and (2) those inclined towards the development of alternative reconstruction strategies seeking to circumvent the limitations associated with standard inverse Fourier methods. In this talk, I will primarily focus on the latter, recounting the last few decades of research into "superresolution" MRSI reconstruction methods, as well as the current state-of-the-art. Jeff Kasten is scientific collaborator at MRI-HUG core of the CIBM. October 2015: "to be determined" by Didier Colin An introductory talk presenting the "PET imaging core" will be given by. Time and Place: 10 am at EPFL, CH-F1-614, add to my calendar Abstract: Didier Colin is scientific collaborator at PET imaging core of the CIBM. Didier Colin is scientific collaborator at PET imaging core of the CIBM. Previous seasons You can find here after the complete list of seminars in previous seasons: BS_seminars_2011_2012.pdf BS_Seminars_2012_2013.pdf BS_seminars_2013_2014.pdf B R E A K FA S T & S C I E N C E C O N TA C T For any question, please contact Dr. Meritxell Bach Cuadra Dr. Nicolas Kunz Dr. Cristina Cudalbu 19/08/15 16:04 Breakfast & Science at CIBM Page 6 of 6 http://www.cibm.ch/breakfast_and_science_cibm The Breakfast & Science seminars aim at boosting scientific exchanges between CIBM cores and at reinforcing the continuous formation of CIBM members. Of course, anyone interested is welcome to attend the seminars. If you want to receive the announcement for the seminars, please subscribe to the CIBM Seminar list. Format: a 10-15 min tutorial basics presentation followed by a 10 min presentation where such concepts are applied to a specific research project. During the scientific discussion following the presentation, a nice breakfast is provided. Time and Venue: Fridays 10-11 am, iteratively at a conference room of the EPFL, CHUV or HUG.
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