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1. Sustainable computational science: the ReScience initiative

Author

Rougier, Nicolas P, Hinsen, Konrad, Alexandre, Frederic, Arildsen, Thomas, Barba, Lorena A, Benureau, Fabien C.Y, Brown, C. Titus, deBuy, Pierre, Caglayan, Ozan, Davison, Andrew P., Delsuc, Marc-Andre, Detorakis, Georgios, Diem, Alexandra, Drix, Damien, Enel, Pierre, Girard, Benoit, Guest, Olivia, Hall, Matt G, Henriques, Rafael N, Hinaut, Xavier, Jaron, Kamil S, Khamassi, Mehdi, Klein, Almar, Manninen, Tiina, Marchesi, Pietro, McGlinn, Daniel, Metzner, Christoph, Petchey, Owen, Plesser, Hans Ekkehard, Poisot, Timothee, Ram, Karthik, Ram, Yoav, Roesch, Etienne, Rossant, Cyrille, Rostami, Vahid, Shifman, Aaron, Stachelek, Joseph, Stimberg, Marcel, Stollmeier, Frank, Vaggi, Federico, Viejo, Guillaume, Vitay, Julien, Vostinar, Anya E, Yurchak, Roman, Zito, Tiziano, Mnemonic Synergy ( Mnemosyne ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut des Maladies Neurodégénératives [Bordeaux] ( IMN ), Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bordeaux ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de biophysique moléculaire ( CBM ), Université d'Orléans ( UO ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Electronic Systems - Aalborg University, Aalborg University [Denmark] ( AAU ), Washington State University ( WSU ), CIM - Communication, Information, Médias - EA 1484 ( CIM ), Université Sorbonne Nouvelle - Paris 3, Université Libre de Bruxelles [Bruxelles] ( ULB ), Laboratoire d'Informatique de l'Université du Mans ( LIUM ), Le Mans Université ( UM ), Ecole des Neurosciences de Paris Île de France ( ENP ), Ecole des Neurosciences de Paris, Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des signaux et systèmes ( L2S ), Université Paris-Sud - Paris 11 ( UP11 ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), University of Southampton [Southampton], Humboldt Universität zu Berlin, Institut cellule souche et cerveau / Stem Cell and Brain Research Institute ( SBRI ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Physiologie de la Perception et de l'Action ( LPPA ), Collège de France ( CdF ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des Systèmes Intelligents et de Robotique ( ISIR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), University of Oxford [Oxford], University College of London [London] ( UCL ), Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Knowledge Technology group [Hamburg] ( KT ), Department of Informatics [Hamburg], Universität Hamburg ( UHH ) -Universität Hamburg ( UHH ), Université de Lausanne ( UNIL ), National Coalition of Independent Scholar ( NCIS ), Finnish Meteorological Institute ( FMI ), Vrije Universiteit Amsterdam [Amsterdam] ( VU ), Department of Biology [Charleston], College of Charleston, Universität Zürich [Zürich] ( UZH ), University of Zürich [Zürich] ( UZH ), Institute of Neuroscience and Medicine [Jülich] ( INM-1 ), Université de Montréal, University of California [Berkeley], Department of Biological Sciences [Stanford], Stanford University [Stanford], Department of Psychology, University of Geneva [Switzerland], Swiss Center for Affective Sciences, University of Ottawa [Ottawa], Michigan State University [East Lansing], Institut de la Vision, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut d'études de la cognition ( IEC ), Département d'Etudes Cognitives - ENS Paris ( DEC ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ), Max Planck Institute of Experimental Medicine [Göttingen] ( MPI ), Statistical Machine Learning and Parsimony ( SIERRA ), Département d'informatique de l'École normale supérieure ( DI-ENS ), École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria de Paris, Institut National de Recherche en Informatique et en Automatique ( Inria ), Chemnitz University of Technology, Grinnell College, Laboratoire pour l'utilisation des lasers intenses ( LULI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -École polytechnique ( X ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Eberhard Karls Universität Tübingen, Mnemonic Synergy (Mnemosyne), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aalborg University [Denmark] (AAU), Washington State University (WSU), University of California [Davis] (UC Davis), University of California (UC), Université libre de Bruxelles (ULB), Laboratoire d'Informatique de l'Université du Mans (LIUM), Le Mans Université (UM), Ecole des Neurosciences de Paris Île de France (ENP), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des signaux et systèmes (L2S), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), University of Southampton, Humboldt University Of Berlin, Institut cellule souche et cerveau (SBRI), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Physiologie de la Perception et de l'Action (LPPA), Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Intelligents et de Robotique (ISIR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), AMAC, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, University College of London [London] (UCL), Instituto de Medicina Molecular (iMM), Faculdade de Medicina [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA)-Universidade de Lisboa = University of Lisbon (ULISBOA), Knowledge Technology group [Hamburg] (KT), University of Hamburg-University of Hamburg, Université de Lausanne = University of Lausanne (UNIL), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Coalition of Independent Scholar (NCIS), Finnish Meteorological Institute (FMI), Vrije Universiteit Amsterdam [Amsterdam] (VU), Universität Zürich [Zürich] = University of Zurich (UZH), Institute of Neuroscience and Medicine [Jülich] (INM-1), Université de Montréal (UdeM), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Biology [Stanford], Stanford University, Université de Genève = University of Geneva (UNIGE), Swiss Center for Affective Sciences (CISA), Michigan State University System, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Labex Institut d'étude de la cognition (IEC), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Max Planck Institute of Experimental Medicine [Göttingen] (MPI), Max-Planck-Gesellschaft, Statistical Machine Learning and Parsimony (SIERRA), Département d'informatique - ENS Paris (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria), Chemnitz University of Technology / Technische Universität Chemnitz, Laboratoire pour l'utilisation des lasers intenses (LULI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of California, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humboldt-Universität zu Berlin, Institut cellule souche et cerveau (U846 Inserm - UCBL1), Universidade de Lisboa (ULISBOA)-Universidade de Lisboa (ULISBOA), Université de Lausanne (UNIL), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Département d'informatique de l'École normale supérieure (DI-ENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Rougier, Nicolas P.

Subjects
FOS: Computer and information sciences, Technology, Journal, lcsh:QA75.5-76.95, Computational Science, GitHub, Scientific Computing and Simulation, Social Computing, Open Science, Replicability, REPRODUCIBLE RESEARCH, [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], Open peer-review, Digital Libraries (cs.DL), Computational science, Open science, Publication, Reproducible, Replicable, Sustainable, GitHub, Open peer-review, [ INFO.INFO-DL ] Computer Science [cs]/Digital Libraries [cs.DL], Science & Technology, Computer Science, Information Systems, Data Science, Computational science, bepress|Physical Sciences and Mathematics|Computer Sciences, Computer Science - Digital Libraries, Sustainable, Reproducibility, Networking and Information Technology R&D (NITRD), Digital Libraries, Computer Science, Reproducible, Publication, Open science, lcsh:Electronic computers. Computer science, [INFO.INFO-DL] Computer Science [cs]/Digital Libraries [cs.DL], Replicable
Abstract

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests., 8 pages, 1 figure

Published
2017
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2. Motion Calculations on Stent Grafts in AAA

Author

Klein, Almar, Renema, W. Klaas Jan, van der Vliet, J. Adam, Oostveen, Luuk J., Hoogeveen, Yvonne, Schultze Kool, Leo J., Slump, Cornelis H., Grundmann, R.T., and Technical Medicine

Subjects
medicine.medical_specialty, Registration, EWI-20532, Computer science, IR-78099, Image Processing, medicine.medical_treatment, Stent, Long term results, Multiple methods, equipment and supplies, medicine.disease, Aortic repair, Abdominal aortic aneurysm, Aneurysm rupture, Motion, Segmentation, abdominal aortic aneurysm, surgical procedures, operative, METIS-278804, Stent graft, medicine, In patient, cardiovascular diseases, Radiology
Abstract

Endovascular aortic repair (EVAR) is a technique which uses stent grafts to treat aortic aneurysms in patients at risk of aneurysm rupture. Although this technique has been shown to be very successful on the short term, the long term results are less optimistic due to failure of the stent graft. The pulsating blood flow applies stresses and forces to the stent graft, which can cause problems such as breakage, leakage, and migration. Therefore it is of importance to gain more insight into the in vivo motion behavior of these devices. If we know more about the motion patterns in well-behaved stent graft as well as ill-behaving devices, we shall be better able to distinguish between these type of behaviors These insights will enable us to detect stent-related problems and might even be used to predict problems beforehand. Further, these insights will help in designing the next generation stent grafts. Firstly, this work discusses the applicability of ECG-gated CT for measuring the motions of stent grafts in AAA. Secondly, multiple methods to segment the stent graft from these data are discussed. Thirdly, this work proposes a method that uses image registration to apply motion to the segmented stent model

Published
2011
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3. Multimodal image registration by edge attraction and regularization using a B-spline grid

Author

Klein, Almar, Kroon, Dirk-Jan, Hoogeveen, Yvonne, Schultze Kool, Leo J., Renema, W. Klaas Jan, Slump, Cornelis H., Dawant, Denoit M., Haynor, David R., and Faculty of Science and Technology

Subjects
Pixel, EWI-19793, business.industry, Computer science, B-spline, Coordinate system, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Image registration, brainweb, Grid, Regularization (mathematics), IR-76403, Weighting, B-spline grid, Robustness (computer science), Computer Science::Computer Vision and Pattern Recognition, Line (geometry), Multimodal, METIS-278704, Computer vision, Artificial intelligence, business, MRI
Abstract

Multi modal image registration enables images from different modalities to be analyzed in the same coordinate system. The class of B-spline-based methods that maximize the Mutual Information between images produce satisfactory result in general, but are often complex and can converge slowly. The popular Demons algorithm, while being fast and easy to implement, produces unrealistic deformation fields and is sensitive to illumination differences between the two images, which makes it unsuitable for multi-modal registration in its original form. We propose a registration algorithm that combines a B-spline grid with deformations driven by image forces. The algorithm is easy to implement and is robust against large differences in the appearance between the images to register. The deformation is driven by attraction-forces between the edges in both images, and a B-spline grid is used to regularize the sparse deformation field. The grid is updated using an original approach by weighting the deformation forces for each pixel individually with the edge strengths. This approach makes the algorithm perform well even if not all corresponding edges are present. We report preliminary results by applying the proposed algorithm to a set of (multi-modal) test images. The results show that the proposed method performs well, but is less accurate than state of the art registration methods based on Mutual Information. In addition, the algorithm is used to register test images to manually drawn line images in order to demonstrate the algorithm's robustness.

Published
2011
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4. Diagnostic quality of time-averaged ECG-gated CT data

Author

Klein, Almar, Oostveen, L.J., Greuter, M.J.W., Hoogeveen, Y., Schultze Kool, L.J., Slump, Cornelis H., Renema, W.K.J., Samei, Ehsan, and Hsieh, Jiang

Subjects
METIS-263817, Frequency response, Image quality, Computer science, Imaging phantom, Aneurysm, ECG gating, medicine, Computer vision, medicine.diagnostic_test, Cardiac cycle, business.industry, METR, medicine.disease, EWI-15294, Abdominal aortic aneurysm, Visualization, medicine.anatomical_structure, Abdomen, IR-65465, Artificial intelligence, Noise (video), business, Electrocardiography, Volume (compression), Biomedical engineering, CT
Abstract

Purpose: ECG-gated CTA allows visualization of the aneurysm and stentgraft during the different phases of the cardiac cycle, although with a lower SNR per cardiac phase than without ECG gating using the same dose. In our institution, abdominal aortic aneurysm (AAA) is evaluated using non-ECG-gated CTA. Some common CT scanners cannot reconstruct a non-gated volume from ECG-gated acquired data. In order to obtain the same diagnostic image quality, we propose off-line temporal averaging of the ECG-gated data. This process, though straightforward, is fundamentally different from taking a non-gated scan, and its result will certainly differ as well. The purpose of this study is to quantitatively investigate how good off-line averaging approximates a non-gated scan. Method: Non-gated and ECG-gated CT scans have been performed on a phantom (Catphan 500). Afterwards the phases of the ECG-gated CTA data were averaged to create a third dataset. The three sets are compared with respect to noise prop-erties (NPS) and frequency response (MTF). To study motion artifacts identical scans were acquired on a programmable dynamic phantom. Results and Conclusions: The experiments show that the spatial frequency content is not affected by the averaging process. The minor differences observed for the noise properties and motion artifacts are in favor of the averaged data. Therefore the averaged ECG-gated phases can be used for diagnosis. This enables the use of ECG-gating for research on stentgrafts in AAA, without impairing clinical patient care.

Published
2009
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5. A segmentation method for stentgrafts in the abdominal aorta from ECG-gated CTA data

Author

Klein, Almar, Renema, W.K.J., Oostveen, L.J., Schultze Kool, L.J., Slump, Cornelis H., Hu, X.P., and Clough, A.V.

Subjects
medicine.medical_specialty, Motion analysis, Cardiac cycle, Computer science, medicine.medical_treatment, Abdominal aorta, Streak, Stent, Aneurysm rupture, METIS-250916, medicine.anatomical_structure, EWI-12134, medicine.artery, medicine, Abdomen, Segmentation, Radiology, Noise (video), IR-62225, Biomedical engineering
Abstract

Endovascular aortic replacement (EVAR) is an established technique, which uses stentgrafts to treat aortic aneurysms in patients at risk of aneurysm rupture. The long-term durability of a stentgraft is affected by the stresses and hemodynamic forces applied to it, and may be reflected by the movements of the stentgraft itself during the cardiac cycle. A conventional CT scan (which results in a 3D volume) is not able to visualize these movements. However, applying ECG-gating does provide insight in the motion of the stentgraft caused by hemodynamic forces at different phases of the cardiac cycle. The amount of data obtained is a factor of ten larger compared to conventional CT, but the radiation dose is kept similar for patient safety. This causes the data to be noisy, and streak artifacts are more common. Algorithms for automatic stentgraft detection must be able to cope with this. Segmentation of the stentgraft is performed by examining slices perpendicular to the centreline. Regions with high CT-values exist at the locations where the metallic frame penetrates the slice. These regions are well suited for detection and sub-pixel localization. Spurious points can be removed by means of a clustering algorithm, leaving only points on the contour of the stent. We compare the performance of several different point detection methods and clustering algorithms. The position of the stent’s centreline is calculated by fitting a circle through these points. The proposed method can detect several stentgraft types, and is robust against noise and streak artifacts.

Published
2008
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