{"id":29,"date":"2016-06-13T11:09:46","date_gmt":"2016-06-13T10:09:46","guid":{"rendered":"http:\/\/eubias.org\/NEUBIAS\/?page_id=29"},"modified":"2016-06-23T14:59:47","modified_gmt":"2016-06-23T13:59:47","slug":"global-planning","status":"publish","type":"page","link":"https:\/\/eubias.org\/NEUBIAS\/venue\/global-planning\/","title":{"rendered":"Key Concepts"},"content":{"rendered":"<div id=\"pl-29\"  class=\"panel-layout\" ><div id=\"pg-29-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-29-0-0\"  class=\"panel-grid-cell\" ><div id=\"panel-29-0-0-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"0\" ><div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-editor so-widget-sow-editor-base\"\n\t\t\t\n\t\t>\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<p style=\"text-align: justify;\">We introduce\u00a0key concepts and keywords of NEUBIAS\u00a0in this page. How these concepts are structured in the network is explained in the\u00a0<a href=\"http:\/\/eubias.org\/NEUBIAS\/?page_id=180\"><strong>NEUBIAS\u00a0Action\u00a0<\/strong>page<\/a>.<\/p>\n<h2 style=\"text-align: justify;\">Bioimage Analysis (BIAS)<\/h2>\n<p style=\"text-align: justify;\">Digital image analysis generally aims at designing computer algorithms to mimic the human recognition of patterns and contexts in order to let computers \"understand\" images. In turn <strong>Bioimage analysis<\/strong> focuses on the quantitative measurement of biological systems by processing multidimensional image data. It hence aims at being as objective as possible in measuring Bioimages and estimating the underlying numerical parameters of the biological systems they capture, independently of human observation.<br \/> <a name=\"components\"><\/a><\/p>\n<h2 style=\"text-align: justify;\">Bioimage Analysts<\/h2>\n<p style=\"text-align: justify;\">We consider that bioimaging involves four different types of expertise.<\/p>\n<ul style=\"text-align: justify;\">\n<li><strong>Life Scientists<\/strong> (e.g. Biologists)\u00a0 ask questions and seek answer by setting up experiments.<\/li>\n<li><strong>Instrumentalists<\/strong> (e.g. Microscopists) develop optical\u00a0systems, collaborate and provide support for the acquisition of BioImage data.<\/li>\n<li><strong>Developers <\/strong>(e.g.\u00a0Image processing algorithm developers, programmers and computer scientists) provide novel algorithms and their implementations to process images.<\/li>\n<li><strong>Bioimage analysts<\/strong> are a new type of experts in BioImaging, they select appropriate\u00a0image processing algorithms and their implementations, and assemble them for\u00a0conducting practical Bioimage Analysis.<\/li>\n<\/ul>\n<p style=\"text-align: justify;\">One of the aim of <strong>NEUBIAS<\/strong> is to explicitly promote the mutual communication between these four communities of experts and to establish the role of Bioimage Analysts in Life Science.<br \/> <a name=\"workflows\"><\/a><\/p>\n<\/div>\n<\/div><\/div><\/div><div id=\"pgc-29-0-1\"  class=\"panel-grid-cell\" ><div id=\"panel-29-0-1-0\" class=\"so-panel widget widget_nav_menu panel-first-child panel-last-child\" data-index=\"1\" ><div class=\"menu-about-container\"><ul id=\"menu-about\" class=\"menu\"><li id=\"menu-item-483\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-483\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/global-planning\/\">Key Concepts<\/a><\/li>\n<li id=\"menu-item-484\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-has-children menu-item-484\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/\">Organization<\/a>\n<ul class=\"sub-menu\">\n\t<li id=\"menu-item-485\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-485\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/events-strategy-wg1\/\">Events &#038; Strategy \u2013 WG1<\/a><\/li>\n\t<li id=\"menu-item-486\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-486\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/training-wg2\/\">Training \u2013 WG2<\/a><\/li>\n\t<li id=\"menu-item-487\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-487\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/outreach-inreach-wg3\/\">Outreach and Inreach \u2013 WG3<\/a><\/li>\n\t<li id=\"menu-item-488\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-488\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/webtool-wg4\/\">Webtool \u2013 WG4<\/a><\/li>\n\t<li id=\"menu-item-489\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-489\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/benchmarking-sample-datasets-wg5\/\">Benchmarking &#038; Sample Datasets \u2013 WG5<\/a><\/li>\n\t<li id=\"menu-item-490\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-490\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/open-publications-wg6\/\">Open Publications \u2013 WG6<\/a><\/li>\n\t<li id=\"menu-item-491\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-491\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/neubias\/short-term-scientific-missions-career-path\/\">Short Term Scientific Missions &#038; Career Path \u2013 WG7<\/a><\/li>\n<\/ul>\n<\/li>\n<li id=\"menu-item-492\" class=\"menu-item menu-item-type-post_type menu-item-object-page menu-item-492\"><a href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/who-are-we\/\">Members \/ Joining<\/a><\/li>\n<\/ul><\/div><\/div><\/div><\/div><div id=\"pg-29-1\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-29-1-0\"  class=\"panel-grid-cell\" ><div id=\"panel-29-1-0-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"2\" ><div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-editor so-widget-sow-editor-base\"\n\t\t\t\n\t\t>\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<h2 style=\"text-align: justify;\">Components<\/h2>\n<div class=\"mceTemp\" style=\"text-align: justify;\">Implementation of certain image processing \/ analysis algorithms. Each component alone does not solve a Bioimage Analysis problem.\u00a0Following is a list of sample components:<\/div>\n<ul style=\"text-align: justify;\">\n<li>A single menu item in image processing software<\/li>\n<li>A plugin \/ module \/ add-ons.\n<ul>\n<li>Note that for plugins that bundles multiple tools, each tool will be the component and the plugin as a whole cannot be a component. These type of\u00a0plugins \/ modules are considered as\u00a0a\u00a0\"Software package \/ Library\".<\/li>\n<\/ul>\n<\/li>\n<li>A class in a JAVA image processing library.<\/li>\n<\/ul>\n<p style=\"text-align: justify;\"><a name=\"Software\"><\/a><\/p>\n<h2 style=\"text-align: justify;\">Workflows<\/h2>\n<p style=\"text-align: justify;\">A workflow is a set of c<em>omponents<\/em>\u00a0assembled in some specific order to process bioimages and estimate some numerical parameters relevant to the biological system under study. Workflows take image data as input and output either processed images or numerical values. Workflows can be a combination of\u00a0\u00a0<em>components<\/em> from the same or different software packages and can for example come under the form of:<\/p>\n<ul style=\"text-align: justify;\">\n<li>A\u00a0script, that calls components in a sequence.<\/li>\n<li>A\u00a0detailed step-by-step instruction on how to chain a sequence of components.<\/li>\n<\/ul>\n<p style=\"text-align: justify;\">Since workflows focus on solving specific problems in life science research project, they are often not generic. The unique aspect of\u00a0<strong>NEUBIAS trainings<\/strong>\u00a0is that they promote students to learn\u00a0how to build their own workflows and customize existing workflows to solve concrete research projects. A workflow written as a script is a reproducible form of bioimage analysis, it is an objective protocol documentation.<br \/> <a name=\"webtool\"><\/a><\/p>\n<h2 style=\"text-align: justify;\">Software\/Libraries<\/h2>\n<p style=\"text-align: justify;\">A package of <em>components<\/em> with an interface to use those components to construct workflows. Software \/ Libraries do not contain specific workflow. For example, ImageJ is a package of various image processing functions, <em>components<\/em>, but it cannot automatically generate a <em>workflow<\/em> for you because each\u00a0<em>workflow<\/em>\u00a0is project specific and unique.<br \/> <a name=\"taggathon\"><\/a><\/p>\n<\/div>\n<\/div><\/div><\/div><div id=\"pgc-29-1-1\"  class=\"panel-grid-cell\" ><div id=\"panel-29-1-1-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"3\" ><div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-editor so-widget-sow-editor-base\"\n\t\t\t\n\t\t>\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<div id=\"attachment_617\" style=\"width: 226px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/simpleBIAS.png\"><img aria-describedby=\"caption-attachment-617\" class=\"size-medium wp-image-617\" src=\"http:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/simpleBIAS-216x300.png\" alt=\"Components in the context of a workflow for bioimage analysis. \" width=\"216\" height=\"300\" srcset=\"https:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/simpleBIAS-216x300.png 216w, https:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/simpleBIAS.png 497w\" sizes=\"(max-width: 216px) 100vw, 216px\" \/><\/a><p id=\"caption-attachment-617\" class=\"wp-caption-text\">Components in the context of a workflow for bioimage analysis.<\/p><\/div>\n<\/div>\n<\/div><\/div><\/div><\/div><div id=\"pg-29-2\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-29-2-0\"  class=\"panel-grid-cell\" ><div id=\"panel-29-2-0-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"4\" ><div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-editor so-widget-sow-editor-base\"\n\t\t\t\n\t\t>\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<h2 style=\"text-align: justify;\">Webtool<\/h2>\n<p style=\"text-align: justify;\">In Internet, we can find many freely offered\u00a0<em>components<\/em>\u00a0for bioimage analysis. By collecting <em>components<\/em> from here and there, we can\u00a0construct our custom \u00a0<em>workflow.<\/em>\u00a0This process might sound straightforward to you but in reality\u00a0we often\u00a0find\u00a0multiple hits of <em>component<\/em>\u00a0having seemingly similar function, which in turn makes the choice difficult to construct <em>one's own\u00a0workflow<\/em>.\u00a0Documentations can\u00a0be too poor to know the algorithm they implement, or to know how easy it is to use.\u00a0To assess the difference of similar implementations, we sometimes even need to\u00a0read the code to know\u00a0their details. At the same time usage examples of <em>components<\/em> in certain\u00a0<em>workflow<\/em>\u00a0is often difficult to find, making it difficult to start.<\/p>\n<p style=\"text-align: justify;\">For this reason, one of the main project of\u00a0NEUBIAS \u00a0is to construct a searchable knowledge base as a web platform . We will commonly call\u00a0this platform \"<strong>Webtool<\/strong>\", its project name is \"<strong>BioImage Informatics Search Engine<\/strong> (<strong>BISE<\/strong>)\". This knowledge base will be fed with content by the community from crowdsourcing and will enable community-driven collaboration and feedback.<\/p>\n<h2 style=\"text-align: justify;\">Taggathon<\/h2>\n<p style=\"text-align: justify;\">Since the\u00a0number of available <em>components<\/em> and <em>workflows<\/em> publicly offered is increasing on a daily basis, the content of the <em>webtool<\/em> needs to be updated constantly. At the same time, the <em>webtool<\/em> itself needs a considerable amount of effort for its infrastructure development. \u00a0A <strong>Taggathon<\/strong> is a strategic event where <em>bioimage analysts and developers<\/em>\u00a0meet physically and work together to feed\u00a0and tag information of <em>components<\/em> and <em>workflows<\/em> into the <em>Webtool <\/em>manually, and also develop its functionalities and discuss about future development and interesting content to include. The word <strong>Taggathon<\/strong> was invented in 2013 by NEUBIAS members, the first one of which\u00a0was held in October 2013 and led to a pilot platform available at <a href=\"http:\/\/biii.info\">http:\/\/biii.info<\/a>. For more details, read\u00a0<a href=\"http:\/\/eubias.org\/NEUBIAS\/?page_id=226\">Taggathon<\/a>\u00a0page.<\/p>\n<h2 style=\"text-align: justify;\">Workgroups<\/h2>\n<p style=\"text-align: justify;\"><strong>NEUBIAS<\/strong> is a network to transform these concepts into actions by structuring them in the same context to enable a better bioimage analysis environment for the Life Science community.\u00a0To facilitate this task, NEUBIAS\u00a0divides its work into seven <strong>Workgroups<\/strong>. Each group will work on concrete deliverables (e.g. activities, events, online resource, webtool, publication...).<\/p>\n<\/div>\n<\/div><\/div><\/div><div id=\"pgc-29-2-1\"  class=\"panel-grid-cell\" ><div id=\"panel-29-2-1-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"5\" ><div\n\t\t\t\n\t\t\tclass=\"so-widget-sow-editor so-widget-sow-editor-base\"\n\t\t\t\n\t\t>\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<div id=\"attachment_614\" style=\"width: 310px\" class=\"wp-caption alignright\"><a href=\"http:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/webtool_schema.png\"><img aria-describedby=\"caption-attachment-614\" loading=\"lazy\" class=\"size-medium wp-image-614\" src=\"http:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/webtool_schema-300x166.png\" alt=\"The knowledge structure and the access-flow of the webtool. Linking between workflow pages (biological entity) and  component pages (image processing entity) bridges the two disciplines. \" width=\"300\" height=\"166\" srcset=\"https:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/webtool_schema-300x166.png 300w, https:\/\/eubias.org\/NEUBIAS\/wp-content\/uploads\/2016\/06\/webtool_schema.png 709w\" sizes=\"(max-width: 300px) 100vw, 300px\" \/><\/a><p id=\"caption-attachment-614\" class=\"wp-caption-text\">The knowledge structure and the access-flow of the webtool. Linking between workflow pages (biological entity) and component pages (image processing entity) bridges the two disciplines.<\/p><\/div>\n<\/div>\n<\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>We introduce\u00a0key concepts and keywords of NEUBIAS\u00a0in this page. How these concepts are structured in the network is explained in the\u00a0NEUBIAS\u00a0Action\u00a0page.Bioimage Analysis (BIAS)Digital image analysis generally aims at designing computer algorithms to mimic the human recognition of patterns and contexts in order to let computers &#8220;understand&#8221; images. In turn Bioimage analysis focuses on the quantitative measurement of biological systems by processing multidimensional image data. It hence aims at being as objective as possible in measuring [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":26,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v20.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Key Concepts - NEUBIAS: Network of BioImage Analysts<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/eubias.org\/NEUBIAS\/venue\/global-planning\/\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"5 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/eubias.org\/NEUBIAS\/venue\/global-planning\/\",\"url\":\"https:\/\/eubias.org\/NEUBIAS\/venue\/global-planning\/\",\"name\":\"Key Concepts - 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