{"id":56931,"date":"2023-03-23T12:41:37","date_gmt":"2023-03-23T10:41:37","guid":{"rendered":"https:\/\/www.iemn.fr\/?p=56931"},"modified":"2023-03-23T12:41:37","modified_gmt":"2023-03-23T10:41:37","slug":"these-yang-z-h-developpement-doutils-de-precision-bases-sur-lapprentissage-profond-pour-lanalyse-des-parasites-malaria-et-cryptosporidium-a-partir-dimages-microscopiques","status":"publish","type":"post","link":"https:\/\/www.iemn.fr\/en\/theses-2022\/these-yang-z-h-developpement-doutils-de-precision-bases-sur-lapprentissage-profond-pour-lanalyse-des-parasites-malaria-et-cryptosporidium-a-partir-dimages-microscopiques.html","title":{"rendered":"THESE YANG Z.H \u00ab\u00a0D\u00e9veloppement d&rsquo;outils de pr\u00e9cision bas\u00e9s sur l&rsquo;apprentissage profond pour l&rsquo;analyse des parasites Malaria et Cryptosporidium \u00e0 partir d&rsquo;images microscopiques \u00ab\u00a0"},"content":{"rendered":"<div id='layer_slider_1'  class='avia-layerslider main_color avia-shadow  avia-builder-el-0  el_before_av_heading  avia-builder-el-first  container_wrap sidebar_right'  style='height: 261px;'  ><div id=\"layerslider_58_5dx2fi8g07yh\" data-ls-slug=\"homepageslider\" class=\"ls-wp-container fitvidsignore ls-selectable\" style=\"width:1140px;height:260px;margin:0 auto;margin-bottom: 0px;\"><div class=\"ls-slide\" data-ls=\"duration:6000;transition2d:5;\"><img loading=\"lazy\" decoding=\"async\" width=\"2600\" height=\"270\" src=\"https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1.jpg\" class=\"ls-bg\" alt=\"\" srcset=\"https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1.jpg 2600w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-300x31.jpg 300w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-768x80.jpg 768w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-1030x107.jpg 1030w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-1500x156.jpg 1500w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-705x73.jpg 705w\" sizes=\"auto, (max-width: 2600px) 100vw, 2600px\" \/><ls-layer style=\"font-size:14px;text-align:left;font-style:normal;text-decoration:none;text-transform:none;font-weight:700;letter-spacing:0px;border-style:solid;border-color:#000;background-position:0% 0%;background-repeat:no-repeat;width:180px;height:30px;left:0px;top:231px;line-height:32px;color:#ffffff;border-radius:6px 6px 6px 6px;padding-left:50px;background-color:rgba(0, 0, 0, 0.57);\" class=\"ls-l ls-ib-icon ls-text-layer\" data-ls=\"minfontsize:0;minmobilefontsize:0;\"><i class=\"fa fa-quote-right\" style=\"color:#ffffff;margin-right:0.8em;font-size:1em;transform:translateY( -0.125em );\"><\/i>ACTUALITES<\/ls-layer><\/div><\/div><\/div><div id='after_layer_slider_1'  class='main_color av_default_container_wrap container_wrap sidebar_right'  ><div class='container av-section-cont-open' ><div class='template-page content  av-content-small alpha units'><div class='post-entry post-entry-type-page post-entry-56931'><div class='entry-content-wrapper clearfix'>\n\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-lfkzefpr-83ebf42e35f6c02b9b444b37bb491446\">\n#top .av-special-heading.av-lfkzefpr-83ebf42e35f6c02b9b444b37bb491446{\nmargin:0 0 10px 0;\npadding-bottom:4px;\n}\nbody .av-special-heading.av-lfkzefpr-83ebf42e35f6c02b9b444b37bb491446 .av-special-heading-tag .heading-char{\nfont-size:25px;\n}\n.av-special-heading.av-lfkzefpr-83ebf42e35f6c02b9b444b37bb491446 .av-subheading{\nfont-size:15px;\n}\n<\/style>\n<div  class='av-special-heading av-lfkzefpr-83ebf42e35f6c02b9b444b37bb491446 av-special-heading-h2  avia-builder-el-1  el_after_av_layerslider  el_before_av_hr  avia-builder-el-first'><h2 class='av-special-heading-tag'  itemprop=\"headline\"  >THESE YANG Z.H \u00ab\u00a0D\u00e9veloppement d\u2018outils de pr\u00e9cision bas\u00e9s sur l\u2019apprentissage profond pour l\u2018analyse des parasites Malaria et Cryptosporidium \u00e0 partir d\u2019images microscopiques \u00ab\u00a0<\/h2><div class=\"special-heading-border\"><div class=\"special-heading-inner-border\"><\/div><\/div><\/div>\n\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-18u73nj-dad6a947580930e400fc42ba200e80f1\">\n#top .hr.av-18u73nj-dad6a947580930e400fc42ba200e80f1{\nmargin-top:5px;\nmargin-bottom:5px;\n}\n.hr.av-18u73nj-dad6a947580930e400fc42ba200e80f1 .hr-inner{\nwidth:100%;\n}\n<\/style>\n<div  class='hr av-18u73nj-dad6a947580930e400fc42ba200e80f1 hr-custom  avia-builder-el-2  el_after_av_heading  el_before_av_textblock  hr-left hr-icon-no'><span class='hr-inner inner-border-av-border-thin'><span class=\"hr-inner-style\"><\/span><\/span><\/div>\n<section  class='av_textblock_section av-jriy64i8-2f4600354c0449b610997916bbd9b6bc'   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/BlogPosting\" itemprop=\"blogPost\" ><div class='avia_textblock'  itemprop=\"text\" >\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-13ewzjw-68e036126b913e5028f77311dc66b825\">\n.av_font_icon.av-13ewzjw-68e036126b913e5028f77311dc66b825{\ncolor:#bfbfbf;\nborder-color:#bfbfbf;\n}\n.av_font_icon.av-13ewzjw-68e036126b913e5028f77311dc66b825 .av-icon-char{\nfont-size:60px;\nline-height:60px;\n}\n<\/style>\n<span  class='av_font_icon av-13ewzjw-68e036126b913e5028f77311dc66b825 avia_animate_when_visible av-icon-style- avia-icon-pos-left avia-icon-animate'><span class='av-icon-char' aria-hidden='true' data-av_icon='\ue8c9' data-av_iconfont='entypo-fontello' ><\/span><\/span>\n<p><strong>Z.H\u00a0 YANG<\/strong><\/p>\n<p>Soutenance : 5 d\u00e9cembre 2022<strong><br \/>\n<\/strong>Th\u00e8se de doctorat en Electronique, micro\u00e9lectronique, nano\u00e9lectronique et micro-ondes, Universit\u00e9 de Lille, ENGSYS Sciences de l\u2019ing\u00e9nierie et des syst\u00e8mes,<\/p>\n<\/div><\/section>\n<section  class='av_textblock_section av-jtefqx33-628129dba2299b2ecd65ebfc92eac29d'   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/BlogPosting\" itemprop=\"blogPost\" ><div class='avia_textblock'  itemprop=\"text\" ><div  class='hr av-kjh3zw-4dff888f744b728a1aca9b3a0971493a hr-default  avia-builder-el-6  avia-builder-el-no-sibling'><span class='hr-inner'><span class=\"hr-inner-style\"><\/span><\/span><\/div>\n<h5>Summary:<\/h5>\n<p>Dans cette th\u00e8se, nous avons propos\u00e9 deux contributions principales li\u00e9es \u00e0 l\u2019analyse par apprentissage profond des parasites Malaria et Cryptosporidium \u00e0 partir d\u2019images microscopiques. Plus sp\u00e9cifiquement, dans la premi\u00e8re contribution, nous avons propos\u00e9 un framework pour diagnostiquer une infection par le parasite Malaria chez les humains en utilisant des images microscopiques de frottis sanguins fins. Compar\u00e9 aux m\u00e9thodes de l\u2019\u00e9tat de l\u2019art, notre framework est bas\u00e9 sur des approches de segmentation et de classification permettant l\u2019analyse directe du parasite au lieu de la cellule qui le contient. Dans ce sens, le framework permet de segmenter directement le parasite Malaria et de distinguer son esp\u00e8ce parmi quatre classes principales : P. Falciparum, P. Ovale, P. Malaria et P. Vivax. Nous d\u00e9montrons l\u2019efficacit\u00e9 de notre framework et notamment son potentiel de g\u00e9n\u00e9ralisation sur des donn\u00e9es interclasses en exploitant plusieurs jeux de donn\u00e9es publiques. De plus, nous montrons que la technique d\u2019augmentation des donn\u00e9es que nous proposons, appel\u00e9e Local Parasite Texture Scanning (LPTS), am\u00e9liore davantage la pr\u00e9cision de notre mod\u00e8le de classification. Dans la deuxi\u00e8me contribution, nous avons propos\u00e9 un framework pour diagnostiquer une infection par le parasite Cryptosporidium chez les vaches laiti\u00e8res en utilisant des images microscopiques de fluorescence. \u00c0 cette fin, nous avons propos\u00e9 une m\u00e9thodologie originale de segmentation des parasites bas\u00e9e sur une approche grossi\u00e8re \u00e0 fine, qui atteint une grande pr\u00e9cision sur notre jeu de donn\u00e9es g\u00e9n\u00e9r\u00e9 de Cryptosporidium et qui permet de d\u00e9passer en termes de performance les m\u00e9thodes de segmentation de l\u2019\u00e9tat de l\u2019art. Nous avons \u00e9galement propos\u00e9 un mod\u00e8le de classification \u00e0 haut pouvoir discriminant permettant d\u2019identifier efficacement le stade de vie des parasites parmi 4 stades asexu\u00e9s : oocyste, trophozo\u00efte, m\u00e9ronte, et forme libre. Nous montrons \u00e0 travers une \u00e9tude exp\u00e9rimentale que notre mod\u00e8le atteint une grande pr\u00e9cision en analysant uniquement le parasite lui-m\u00eame et sans avoir besoin d\u2019informations suppl\u00e9mentaires li\u00e9es \u00e0 la taille et au nombre de noyaux qui sont n\u00e9cessaires au biologiste afin de r\u00e9aliser sa classification.<\/p>\n<h5>Abstract:<\/h5>\n<p>In this thesis, we proposed two main contributions related to deep learning analysis of Malaria and Cryptosporidium parasites from microscopic images. More specifically, in the first contribution, we proposed a framework for diagnosing Malaria parasite infection in humans using microscopic images of thin blood smears. Compared to the state of the art methods, our framework is based on segmentation and classification approaches allowing the direct analysis of the parasite instead of the cell that contains it. In this sense, the framework allows to directly segment the Malaria parasite and to distinguish its species among four main classes: P. Falciparum, P. Ovale, P. Malaria and P. Vivax. We demonstrate the efficiency of our framework and in particular its potential for generalization on inter-class data by exploiting several public datasets. Moreover, we show that our proposed data augmentation technique, called Local Parasite Texture Scanning (LPTS), further improves the accuracy of our classification model. In the second contribution, we proposed a framework to diagnose Cryptosporidium parasite infection in dairy cows using fluorescence microscopy images. To this end, we proposed an original parasite segmentation methodology based on a coarse to fine approach, which achieves high accuracy on our generated Cryptosporidium dataset and outperforms state-of-the-art segmentation methods. We have also proposed a classification model with high discriminating power to efficiently identify the life stage of parasites among 4 asexual stages: oocyst, trophozoite, meront, and free form. We show through an experimental study that our model achieves a high accuracy by analyzing only the parasite itself and without the need for additional information related to the size and number of nuclei that are necessary for the biologist to perform its classification.<\/p>\n<\/div><\/section>\n<\/div><\/div><\/div><!-- close content main div --><\/div><\/div><div id='layer_slider_2'  class='avia-layerslider main_color avia-shadow  avia-builder-el-7  el_after_av_textblock  el_before_av_hr  slider-not-first container_wrap sidebar_right'  style='height: 261px;'  ><div id=\"layerslider_58_1i23bwqutodjk\" data-ls-slug=\"homepageslider\" class=\"ls-wp-container fitvidsignore ls-selectable\" style=\"width:1140px;height:260px;margin:0 auto;margin-bottom: 0px;\"><div class=\"ls-slide\" data-ls=\"duration:6000;transition2d:5;\"><img loading=\"lazy\" decoding=\"async\" width=\"2600\" height=\"270\" src=\"https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1.jpg\" class=\"ls-bg\" alt=\"\" srcset=\"https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1.jpg 2600w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-300x31.jpg 300w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-768x80.jpg 768w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-1030x107.jpg 1030w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-1500x156.jpg 1500w, https:\/\/www.iemn.fr\/wp-content\/uploads\/2019\/01\/sliders_news1-705x73.jpg 705w\" sizes=\"auto, (max-width: 2600px) 100vw, 2600px\" \/><ls-layer style=\"font-size:14px;text-align:left;font-style:normal;text-decoration:none;text-transform:none;font-weight:700;letter-spacing:0px;border-style:solid;border-color:#000;background-position:0% 0%;background-repeat:no-repeat;width:180px;height:30px;left:0px;top:231px;line-height:32px;color:#ffffff;border-radius:6px 6px 6px 6px;padding-left:50px;background-color:rgba(0, 0, 0, 0.57);\" class=\"ls-l ls-ib-icon ls-text-layer\" data-ls=\"minfontsize:0;minmobilefontsize:0;\"><i class=\"fa fa-quote-right\" style=\"color:#ffffff;margin-right:0.8em;font-size:1em;transform:translateY( -0.125em );\"><\/i>ACTUALITES<\/ls-layer><\/div><\/div><\/div><div id='after_layer_slider_2'  class='main_color av_default_container_wrap container_wrap sidebar_right'  ><div class='container av-section-cont-open' ><div class='template-page content  av-content-small alpha units'><div class='post-entry post-entry-type-page post-entry-56931'><div class='entry-content-wrapper clearfix'>\n\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-18u73nj-dad6a947580930e400fc42ba200e80f1\">\n#top .hr.av-18u73nj-dad6a947580930e400fc42ba200e80f1{\nmargin-top:5px;\nmargin-bottom:5px;\n}\n.hr.av-18u73nj-dad6a947580930e400fc42ba200e80f1 .hr-inner{\nwidth:100%;\n}\n<\/style>\n<div  class='hr av-18u73nj-dad6a947580930e400fc42ba200e80f1 hr-custom  avia-builder-el-8  el_after_av_layerslider  avia-builder-el-no-sibling  hr-left hr-icon-no'><span class='hr-inner inner-border-av-border-thin'><span class=\"hr-inner-style\"><\/span><\/span><\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":20,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[316],"tags":[],"class_list":["post-56931","post","type-post","status-publish","format-standard","hentry","category-theses-2022"],"_links":{"self":[{"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/posts\/56931","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/users\/20"}],"replies":[{"embeddable":true,"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/comments?post=56931"}],"version-history":[{"count":0,"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/posts\/56931\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/media?parent=56931"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/categories?post=56931"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.iemn.fr\/en\/wp-json\/wp\/v2\/tags?post=56931"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}