Processing and Analysis of Biomedical Information: First International SIPAIM Workshop, SaMBa 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 20, 2018, Revised Selected Papers [1st ed.] 978-3-030-13834-9, 978-3-030-13835-6

Table of contents :
Front Matter ....Pages I-VIII
Front Matter ....Pages 1-1
Identification of U-Bundles Based on Sulcus Morphology (M. Guevara, Z. Y. Sun, P. Guevara, D. Rivière, C. Poupon, J.-F. Mangin)....Pages 3-7
A Method Towards Cerebral Aneurysm Detection in Clinical Settings (Sarada Prasad Dakua, Julien Abinahed, Abdulla Al-Ansari, Pablo Garcia Bermejo, Ayaman Zakaria, Abbes Amira et al.)....Pages 8-15
Common Carotid Artery Lumen Automatic Segmentation from Cine Fast Spin Echo Magnetic Resonance Imaging (Lívia Rodrigues, Roberto Souza, Letícia Rittner, Richard Frayne, Roberto Lotufo)....Pages 16-24
Using Deep Learning to Classify Burnt Body Parts Images for Better Burns Diagnosis (Joohi Chauhan, Rahul Goswami, Puneet Goyal)....Pages 25-32
Mixed-Model Noise Removal in 3D MRI via Rotation-and-Scale Invariant Non-Local Means (Xiangyuan Liu, Quansheng Liu, Zhongke Wu, Xingce Wang, Jose Pozo Sole, Alejandro Frangi)....Pages 33-41
Autism Spectrum Disorders (ASD) Characterization in Children by Decomposing MRI Brain Regions with Zernike Moments (Nicolás Múnera, Javier Almeida, Charlems Álvarez, Nelson Velasco, Eduardo Romero)....Pages 42-53
Front Matter ....Pages 55-55
MP-IDB: The Malaria Parasite Image Database for Image Processing and Analysis (Andrea Loddo, Cecilia Di Ruberto, Michel Kocher, Guy Prod’Hom)....Pages 57-65
An Algorithm for Individual Intermediate Filament Tracking (Dmytro Kotsur, Roman Yakobenchuk, Rudolf E. Leube, Reinhard Windoffer, Julian Mattes)....Pages 66-74
An Automatic Segmentation of Gland Nuclei in Gastric Cancer Based on Local and Contextual Information (Cristian Barrera, Germán Corredor, Sunny Alfonso, Andrés Mosquera, Eduardo Romero)....Pages 75-81
A Transfer Learning Exploited for Indexing Protein Structures from 3D Point Clouds (Halim Benhabiles, Karim Hammoudi, Feryal Windal, Mahmoud Melkemi, Adnane Cabani)....Pages 82-89
Front Matter ....Pages 91-91
Proposal of a Smart Hospital Based on Internet of Things (IoT) Concept (Camilo Cáceres, João Mauricio Rosário, Dario Amaya)....Pages 93-104
A Web-Based Telepathology Framework for Collaborative Work of Pathologists to Support Teaching and Research in Latin America (Darwin Díaz, Germán Corredor, Eduardo Romero, Angel Cruz-Roa)....Pages 105-112
Front Matter ....Pages 113-113
Proposal of Methodology of a Bipedal Humanoid Gait Generation Based on Cognitive Algorithm (João Maurício Rosário, Renato Suekichi Kuteken, Luis Miguel Izquierdo Cordoba)....Pages 115-126
Ocular Control Characterization of Motor Disabilities: The Cerebral Palsy Case (Jully González, Angélica Atehortúa, Ricardo Moncayo, Eduardo Romero)....Pages 127-137
Back Matter ....Pages 139-139

Citation preview

LNCS 11379

Natasha Lepore Jorge Brieva Eduardo Romero Daniel Racoceanu Leo Joskowicz (Eds.)

Processing and Analysis of Biomedical Information First International SIPAIM Workshop, SaMBa 2018 Held in Conjunction with MICCAI 2018 Granada, Spain, September 20, 2018, Revised Selected Papers

123

Lecture Notes in Computer Science Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen

Editorial Board David Hutchison Lancaster University, Lancaster, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Friedemann Mattern ETH Zurich, Zurich, Switzerland John C. Mitchell Stanford University, Stanford, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel C. Pandu Rangan Indian Institute of Technology Madras, Chennai, India Bernhard Steffen TU Dortmund University, Dortmund, Germany Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA

11379

More information about this series at http://www.springer.com/series/7412

Natasha Lepore Jorge Brieva Eduardo Romero Daniel Racoceanu Leo Joskowicz (Eds.) •

•

Processing and Analysis of Biomedical Information First International SIPAIM Workshop, SaMBa 2018 Held in Conjunction with MICCAI 2018 Granada, Spain, September 20, 2018 Revised Selected Papers

123

Editors Natasha Lepore Keck School Medicine of University of Southern California Los Angeles, CA, USA Jorge Brieva Universidad Panamericana Mexico City, Mexico

Daniel Racoceanu Pontificia Universidad Católica del Perú Lima, Peru Leo Joskowicz The Hebrew University of Jerusalem Jerusalem, Israel

Eduardo Romero National University of Colombia Bogotá, Colombia

ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Computer Science ISBN 978-3-030-13834-9 ISBN 978-3-030-13835-6 (eBook) https://doi.org/10.1007/978-3-030-13835-6 Library of Congress Control Number: 2019932167 LNCS Sublibrary: SL6 – Image Processing, Computer Vision, Pattern Recognition, and Graphics © Springer Nature Switzerland AG 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

Medical information and image processing have been experiencing an accelerated growth worldwide in the past decade, and are reaching all parts of the world. In particular, Spanish- and Portuguese-speaking countries in Latin America, which have a long and rich history of academic and clinical research, are addressing a variety of health-care challenges, both general and specific to the region. The scientific communities in these countries have been growing and have attended and organized a growing number of regional and international conferences and meetings. In this context, the International Symposium on Medical Information Processing and Analysis (SIPAIM) is a yearly event held in various Latin American cities. Its main goal is bringing together biomedical engineering and medical researchers from the region with a strong interest in image and signal analysis. This community originated in the late 2000s with a series of collaborative workshops around medical information and image processing. These regular workshops eventually evolved into the International Symposium on Medical Information Processing and Analysis (SIPAIM) in 2009, and resulted in the legal establishment of the SIPAIM society (Sociedad Internacional de Procesamiento y Análisis de la Información Médica) in March 2015. SIPAIM is a non-profit foundation promoting research and academic activities in the field of medical information management and medical imaging by bringing together scientists, engineers, physicians, surgeons, educators, and students mainly, although not exclusively, from Latin American countries. Through these events, SIPAIM has managed to stimulate the emergence of a growing Latin American network related to medical and biomedical information. We are convinced that including the MICCAI community—with its traditional ingenuity and brilliance—in these discussions will help pave the way to a whole set of new scientific challenges, models, and solutions. This year, as a preview to MICCAI 2020 to be held in Lima, Perú, MICCAI hosted the first ever MICCAI-SIPAIM Workshop. Its purpose was to present success stories of science, research and innovation stemming from Latin American and to encourage the formation of international academic networks in biomedical research with a strong component in medical information processing. The workshop was highly successful, with two plenary talks and a panel of four experts from Latin America. In total, 14 papers were submitted and accepted as poster presentations after being peer reviewed (single blind/two reviews per paper). We intend to sustainably support this network and its spirit in coming years, both until MICCAI 2020 and beyond. September 2018

Natasha Lepore Jorge Brieva Eduardo Romero Daniel Racoceanu Leo Joskowicz

Organization

Conference Committee Conference Chairs Natasha Lepore Jorge Brieva Eduardo Romero Daniel Racoceanu Leo Joskowicz

Children’s Hospital Los Angeles University of Southern California, USA Universidad Panamericana, Mexico Universidad Nacional de Colombia, Colombia Pontifical Catholic University of Peru, Peru The Hebrew University of Jerusalem, Israel

Organizing Committee Natasha Lepore Jorge Brieva Eduardo Romero Daniel Racoceanu Juan David García Leo Joskowicz Alejandro Frangi

Children’s Hospital Los Angeles University of Southern California, USA Universidad Panamericana, Mexico Universidad Nacional de Colombia, Colombia Pontifical Catholic University of Peru, Peru Universidad Nacional de Colombia, Colombia The Hebrew University of Jerusalem, Israel University of Leeds, UK

Program Committee Oscar Acosta Carlos Alberola-López Fernando Arambula Niharika Gajawelli Alfredo Hernández Marius Linguraru Diana Mateus Dehaes Mathieu Mauricio Reyes Sinchai Tsao Demian Wassermann

Université de Rennes 1, France Universidad de Valladolid, Spain Universidad Nacional Autonoma de Mexico, Mexico Children’s Hospital Los Angeles, USA Institut National de la Santé et de la Recherche Médicale, France Children’s National Health System, USA Technical University of Munich, Germany Université de Montréal, Canada University of Bern, Switzerland Children’s Hospital Los Angeles, USA Inria, France

Contents

Medical Imaging Identification of U-Bundles Based on Sulcus Morphology . . . . . . . . . . . . . . M. Guevara, Z. Y. Sun, P. Guevara, D. Rivière, C. Poupon, and J.-F. Mangin

3

A Method Towards Cerebral Aneurysm Detection in Clinical Settings . . . . . . Sarada Prasad Dakua, Julien Abinahed, Abdulla Al-Ansari, Pablo Garcia Bermejo, Ayaman Zakaria, Abbes Amira, and Faycal Bensaali

8

Common Carotid Artery Lumen Automatic Segmentation from Cine Fast Spin Echo Magnetic Resonance Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . Lívia Rodrigues, Roberto Souza, Letícia Rittner, Richard Frayne, and Roberto Lotufo Using Deep Learning to Classify Burnt Body Parts Images for Better Burns Diagnosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Joohi Chauhan, Rahul Goswami, and Puneet Goyal Mixed-Model Noise Removal in 3D MRI via Rotation-and-Scale Invariant Non-Local Means . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Xiangyuan Liu, Quansheng Liu, Zhongke Wu, Xingce Wang, Jose Pozo Sole, and Alejandro Frangi Autism Spectrum Disorders (ASD) Characterization in Children by Decomposing MRI Brain Regions with Zernike Moments . . . . . . . . . . . . Nicolás Múnera, Javier Almeida, Charlems Álvarez, Nelson Velasco, and Eduardo Romero

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25

33

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Digital Pathology MP-IDB: The Malaria Parasite Image Database for Image Processing and Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Andrea Loddo, Cecilia Di Ruberto, Michel Kocher, and Guy Prod’Hom An Algorithm for Individual Intermediate Filament Tracking . . . . . . . . . . . . Dmytro Kotsur, Roman Yakobenchuk, Rudolf E. Leube, Reinhard Windoffer, and Julian Mattes

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Contents

An Automatic Segmentation of Gland Nuclei in Gastric Cancer Based on Local and Contextual Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cristian Barrera, Germán Corredor, Sunny Alfonso, Andrés Mosquera, and Eduardo Romero A Transfer Learning Exploited for Indexing Protein Structures from 3D Point Clouds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Halim Benhabiles, Karim Hammoudi, Feryal Windal, Mahmoud Melkemi, and Adnane Cabani

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E-Health Proposal of a Smart Hospital Based on Internet of Things (IoT) Concept . . . . Camilo Cáceres, João Mauricio Rosário, and Dario Amaya A Web-Based Telepathology Framework for Collaborative Work of Pathologists to Support Teaching and Research in Latin America . . . . . . . Darwin Díaz, Germán Corredor, Eduardo Romero, and Angel Cruz-Roa

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Motor Analysis and Biosignals Proposal of Methodology of a Bipedal Humanoid Gait Generation Based on Cognitive Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . João Maurício Rosário, Renato Suekichi Kuteken, and Luis Miguel Izquierdo Cordoba Ocular Control Characterization of Motor Disabilities: The Cerebral Palsy Case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Jully González, Angélica Atehortúa, Ricardo Moncayo, and Eduardo Romero Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Medical Imaging

Identification of U-Bundles Based on Sulcus Morphology M. Guevara1(&), Z. Y. Sun1, P. Guevara3, D. Rivière1, C. Poupon2, and J.-F. Mangin1 1

2

UNATI Neurospin, CEA, Université Paris-Saclay, Gif-sur-Yvette, France [email protected] UNIRS Neurospin, CEA, Université Paris-Saclay, Gif-sur-Yvette, France 3 Universidad de Concepción, Concepción, Chile

1 Introduction It is a fact that the brain cortical folding pattern morphology is specific to each human being. Neuroanatomists think that the folding pattern is strongly related to brain connectivity [1]. As each folding variation implies a specific rearrangement of the different white matter bundles, it also impacts the position of functional regions. This particularity raises an issue for precise brain spatial normalization, as nobody knows how to align brains with different folding patterns. For this reason, in the field of brain segmentation, old fashion approaches relying on a single model, often generated from a single subject or a group’s average, cannot overcome the folding variability. Therefore, modern strategies are often built from a multi-subject atlas, which has proven to be a very efficient solution to overcome this difficulty [2]. In order to design an analogous solution for brain mapping, it was recently proposed to restrict statistical analysis to groups of subjects with compatible folding pattern [3], which has been experimented to deal with the impact of the central sulcus morphology on fMRI-based activation maps [4]. Differences in the cortical folding have been proved to be associated with differences in the localization of functional areas. Therefore, we need to understand better how to relate to each other brains with different folding patterns. In this abstract, we propose a new step in this direction: we performed a first attempt to observe an effect of a simple morphological polymorphism related to central sulcus on the underlying U-fiber organization.

2 Method We studied the impact of the left central sulcus on the neighboring short bundles. The central sulcus is one of the most stable and prominent of the human brain, which makes it can be identified without ambiguity, and it presents a precise structure-function landmark called the “hand knob” [4]. We used 71 healthy subjects from the ARCHI database (23.5 ± 5.2 years old of age; 44 males, 27 females; 68 right-handed and 3 left-handed) [5]. First, the isomap of the central sulcus is calculated with the method © Springer Nature Switzerland AG 2019 N. Lepore et al. (Eds.): SaMBa 2018, LNCS 11379, pp. 3–7, 2019. https://doi.org/10.1007/978-3-030-13835-6_1

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described in [4], obtaining an axis of variability that goes from a “single knob” configuration to a “double knob” configuration (Fig. 1). After affine spatial normalization, the tractograms (i.e. sets of streamlines) of all subjects were further aligned in order to register all central sulci toward the most neutral sulcus i.e. the one with the shape that minimizes the average distance to the rest. Subjects were then gathered in morphologically compatible groups by dividing the isomap axis into 6 intervals of the same length. Subjects of each group did not overlap between them. To each group we applied a slight variation of the method described in [6] in order to identify reproducible short white matter bundles among the subjects (Fig. 2). Briefly, accordingly to the Desikan-Killiany atlas [7], we selected the ROIs around the central sulcus (namely precentral (PrC), postcentral (PoC), caudal middle frontal (CMF), pars opercularis (Op), superior parietal (SP), supramarginal (SM) gyri) and extracted the fibers connecting each pair of them. Then to the extracted sub-tractograms we applied an intrasubject average-link hierarchical agglomerative clustering in order to identify actual fiber bundles (i.e. fibers with similar shape and position along the gyri). The fiber bundles were then matched across the subjects by means of an inter-subject hierarchical clustering, and at the same time bundles that were no present in at least half of the population were discarded. This results in 6 different “atlases”, each one specific to its group. Then a matching across atlases is performed to assign a common label to similar bundles. In order to do that a mean centroid representing each bundle is calculated. First, a centroid from the first atlas (the most to the left in the isomap) is taken. A nearby centroid is sought from the second atlas, within a distance threshold. If found, a new centroid is calculated from these two, which is used to seek a nearby centroid from the third atlas and so on. If no centroid is found in a particular atlas, it is just skipped. Unlike the original method were only two preliminary atlases were matched to keep only reproducible bundles [6], in this case we sought to identify the presence of the bundles among the atlases, therefore those with no matches are kept but labeled with a single different label. Also, for each bundle, the correlation of fiber coordinates from 5 equidistant points (beginning, a quarter, middle, three quarters and ending) with the isomap values was computed.

Fig. 1. Moving average of the central sulcus morphology.

Identification of U-Bundles Based on Sulcus Morphology

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Fig. 2. Schematic of the U-fiber identification method.

3 Results We computed bundles connecting pairs of 6 regions close to the central sulcus (Fig. 3). From the visual inspection, we identified 6 bundles showing regular changes either in position or shape, along the isomap axis (Fig. 4). Most of these differences correspond to fiber extremities moving up or down as the central sulcus shape shifts. Also, these bundles show a moderate correlation with the sulcus isomap values for at least one section of points, depending on their configuration.

Fig. 3. Bundles obtained with the method.

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We also applied the described method to a different database and selected a higher number of atlas. For a same bundle there seem to exist two different configurations among the groups (Fig. 5).

Bundle PoC-PrC 1

PoC-PrC 2

PoC-SM

PoC-SP

PrC-SM 1

PrC-SM 2

r 0.175 0.165 0.128 0.172 0.172 0.237 0.217 -0.313 -0.032 0.237 0.217 -0.188 0.233 -0.307 -0.395 0.21 0.145 0.057 -0.05 -0.025 0.139 0.184 0.239 0.34 -0.261 0.145 -0.232 0.083 0.122 -0.133

p