{"id":5788,"date":"2024-11-07T07:22:49","date_gmt":"2024-11-07T05:22:49","guid":{"rendered":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=5788"},"modified":"2025-03-14T20:59:26","modified_gmt":"2025-03-14T18:59:26","slug":"bioimage-analysis-fundamentals-2025","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/bioimage-analysis-fundamentals-2025\/","title":{"rendered":"BioImage Analysis Fundamentals \u2013 2025"},"content":{"rendered":"\n<p>This 5-day workshop\u00a0is\u00a0intended to give\u00a0a\u00a0thorough\u00a0introduction to Bioimage analysis\u00a0for\u00a0individuals\u00a0with little to no prior experience but who want\u00a0to\u00a0develop\u00a0some\u00a0basic\u00a0skills in image processing and analysis workflows using both open-source and proprietary software.\u00a0Participants\u00a0will\u00a0get\u00a0hands-on experience with image restoration, segmentation techniques, feature extraction and tracking using classical and advanced machine and deep learning tools. Most importantly, students will gain insight in data visualization and analysis for reproducible research.\u00a0By\u00a0the\u00a0end of the\u00a0workshop,\u00a0attendees will\u00a0have the opportunity to work on\u00a0a final project,\u00a0in\u00a0which\u00a0they will be able\u00a0to apply\u00a0the\u00a0newly\u00a0learned\u00a0skills\u00a0on\u00a0a real-world bioimage analysis challenge.<br><\/p>\n\n\n\n<div class=\"wp-block-uagb-image uagb-block-2453417f wp-block-uagb-image--layout-default wp-block-uagb-image--effect-static wp-block-uagb-image--align-none\"><figure class=\"wp-block-uagb-image__figure\"><img decoding=\"async\" srcset=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/202502_NPO_course_flyer-724x1024.jpg ,https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/202502_NPO_course_flyer-scaled.jpg 780w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/202502_NPO_course_flyer-scaled.jpg 360w\" sizes=\"auto, (max-width: 480px) 150px\" src=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/202502_NPO_course_flyer-724x1024.jpg\" alt=\"\" class=\"uag-image-5789\" width=\"3508\" height=\"4960\" title=\"202502_NPO_course_flyer\" loading=\"lazy\" role=\"img\"\/><\/figure><\/div>\n\n\n\n<div class=\"wp-block-uagb-buttons uagb-buttons__outer-wrap uagb-btn__default-btn uagb-btn-tablet__default-btn uagb-btn-mobile__default-btn uagb-block-566ec058\"><div class=\"uagb-buttons__wrap uagb-buttons-layout-wrap \">\n<div class=\"wp-block-uagb-buttons-child uagb-buttons__outer-wrap uagb-block-c5523c1d wp-block-button\"><div class=\"uagb-button__wrapper\"><a class=\"uagb-buttons-repeater wp-block-button__link\" aria-label=\"\" href=\"https:\/\/forms.gle\/pDLS1fPqkXUYB1Uw9\" rel=\"follow noopener\" target=\"_blank\" role=\"button\"><div class=\"uagb-button__link\">FOR REGISTRATION CLICK HERE<\/div><span class=\"uagb-button__icon uagb-button__icon-position-after\"><svg xmlns=\"https:\/\/www.w3.org\/2000\/svg\" viewBox=\"0 0 448 512\" aria-hidden=\"true\" focussable=\"false\"><path d=\"M438.6 278.6l-160 160C272.4 444.9 264.2 448 256 448s-16.38-3.125-22.62-9.375c-12.5-12.5-12.5-32.75 0-45.25L338.8 288H32C14.33 288 .0016 273.7 .0016 256S14.33 224 32 224h306.8l-105.4-105.4c-12.5-12.5-12.5-32.75 0-45.25s32.75-12.5 45.25 0l160 160C451.1 245.9 451.1 266.1 438.6 278.6z\"><\/path><\/svg><\/span><\/a><\/div><\/div>\n<\/div><\/div>\n\n\n\n<p class=\"has-large-font-size\"><strong>Workshop Objectives<\/strong>:<\/p>\n\n\n\n<p>By the end of this workshop, participants will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Understand foundational microscopy techniques and the principles of bioimage acquisition and analysis.<\/li>\n\n\n\n<li>Apply essential image processing methods, such as thresholding and segmentation, to analyze bioimages effectively.<\/li>\n\n\n\n<li>Use FIJI\/ImageJ for performing detailed image analysis, including stitching, colocalization, and intensity-based comparisons.<\/li>\n\n\n\n<li>Leverage ZEISS arivis for advanced 3D visualization, machine learning-based segmentation, and tracking.<\/li>\n\n\n\n<li>Create reproducible data visualizations and establish workflows for consistent bioimage data management.<\/li>\n\n\n\n<li>Engage in hands-on sessions designed to tackle real-world bioimage analysis challenges.<\/li>\n\n\n\n<li>Connect and collaborate with peers, fostering professional networking and knowledge exchange.<\/li>\n<\/ul>\n\n\n\n<p class=\"has-large-font-size\"><strong>Workshop Agenda<\/strong>:<\/p>\n\n\n\n<p><strong>Day 1: Introduction to Microscopy and Bioimage Analysis<\/strong><br><em>Topics Covered:<\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>9:00 &#8211; 9:15<\/strong> \u2013 Workshop Introduction and Overview<\/li>\n\n\n\n<li><strong>9:15 &#8211; 10:00<\/strong> \u2013 <strong>Introduction to Microscopy Techniques<\/strong>: Principles, types, and applications in bioimaging<\/li>\n\n\n\n<li><strong>10:15 &#8211; 11:20<\/strong> \u2013 <strong>Image Acquisition<\/strong>: Overview of methods followed by a group discussion on bioimage analysis challenges<\/li>\n\n\n\n<li><strong>11:20 &#8211; 12:10<\/strong> \u2013 <strong>Image Preprocessing<\/strong>: Introduction to preprocessing techniques with group practice<\/li>\n\n\n\n<li><strong>12:10 &#8211; 13:10<\/strong> \u2013 <strong>Lunch Break<\/strong><\/li>\n\n\n\n<li><strong>13:10 &#8211; 15:30<\/strong> \u2013 <strong>Introduction to Thresholding and Segmentation<\/strong>\u00a0<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 2: FIJI\/ImageJ<\/strong><br><em>Topics Covered:<\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>9:30 &#8211; 10:15<\/strong> \u2013 <strong>Introduction to FIJI\/ImageJ<\/strong>: Overview of the interface and essential functions<\/li>\n\n\n\n<li><strong>10:30 &#8211; 11:45<\/strong> \u2013 <strong>Basic Analysis Workflows<\/strong>: Hands-on practice with segmentation and GPU-accelerated tools<\/li>\n\n\n\n<li><strong>11:45 &#8211; 12:45<\/strong> \u2013 <strong>Lunch Break<\/strong>\u00a0<\/li>\n\n\n\n<li><strong>12:45 &#8211; 15:30<\/strong> \u2013 <strong>Advanced Processing<\/strong>: Image stitching, intensity quantification, and pixel-based colocalization<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 3: ZEISS arivis<\/strong><br><em>Topics Covered:<\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>9:30 &#8211; 10:30<\/strong> \u2013 <strong>ARIVIS Interface<\/strong>: Introduction to user interface, data import, and setup<\/li>\n\n\n\n<li><strong>10:50 &#8211; 12:00<\/strong> \u2013 <strong>3D Visualization and Segmentation<\/strong>: Practice with data import and visualization<\/li>\n\n\n\n<li><strong>12:00 &#8211; 13:00<\/strong> \u2013 <strong>Lunch Break<\/strong>\u00a0<\/li>\n\n\n\n<li><strong>13:00 &#8211; 15:15<\/strong> \u2013 <strong>Machine Learning in ARIVIS<\/strong>: Hands-on session with Cellpose for ML-based segmentation, colocalization, and tracking<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 4: Data Visualization and Reproducible Science<\/strong><br><em>Topics Covered:<\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>9:00 &#8211; 10:15<\/strong> \u2013 <strong>Data Visualization<\/strong>: Creating effective visuals for data analysis<\/li>\n\n\n\n<li><strong>10:30 &#8211; 11:15<\/strong> \u2013 <strong>Introduction to Reproducible Science<\/strong>: Tips for reproducible workflows<\/li>\n\n\n\n<li><strong>11:50 &#8211; 13:15<\/strong> \u2013 <strong>Lunch Break<\/strong>\u00a0<\/li>\n\n\n\n<li><strong>13:15 &#8211; 15:00<\/strong> \u2013 <strong>Project Work and Preparation<\/strong>: Setting up final projects, defining objectives, and planning steps<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 5: Final Projects and Presentations<\/strong><br><em>Topics Covered:<\/em><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>9:00 &#8211; 15:00<\/strong> \u2013 <strong>Project Work and Presentations<\/strong>: Final project work, uploads, and presentations.<\/li>\n<\/ul>\n\n\n\n<p><em>Lunches and coffee breaks are scheduled, but refreshments are not provided.<\/em><\/p>\n\n\n\n<p class=\"has-medium-font-size\"><strong>Registration<\/strong>: <a href=\"https:\/\/docs.google.com\/forms\/d\/e\/1FAIpQLSeofsek9Z3PUVuicejrdQnCU2MY3SAymyPYrxxFOlyM3a4DAw\/viewform?usp=sf_link\">https:\/\/docs.google.com\/forms\/d\/e\/1FAIpQLSeofsek9Z3PUVuicejrdQnCU2MY3SAymyPYrxxFOlyM3a4DAw\/viewform?usp=sf_link<\/a><\/p>\n\n\n\n<p class=\"has-medium-font-size\"><strong>Preparation<\/strong>:<br>Computers are provided with the necessary software. Materials, including datasets will be provided before the course start.&nbsp;<\/p>\n\n\n\n<p>For questions or more information, contact: VMCF staff &#8211; Judith Garcia Gonzalez (garciagj@natur.cuni.cz)<\/p>\n\n\n\n<p><strong>GitHub<\/strong>: For additional resources, follow us on <a href=\"https:\/\/github.com\/vmcf-konfmi\">GitHub<\/a>.<\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>This 5-day workshop\u00a0is\u00a0intended to give\u00a0a\u00a0thorough\u00a0introduction to Bioimage analysis\u00a0for\u00a0individuals\u00a0with little to no prior experience but who want\u00a0to\u00a0develop\u00a0some\u00a0basic\u00a0skills in image processing and analysis workflows using both open-source and proprietary software.\u00a0Participants\u00a0will\u00a0get\u00a0hands-on experience with image restoration, segmentation techniques, feature extraction and tracking using classical and advanced machine and deep learning tools. Most importantly, students will gain insight in data [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":5790,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","footnotes":""},"categories":[24,22],"tags":[],"class_list":["post-5788","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-courses","category-workshops"],"uagb_featured_image_src":{"full":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled.jpg",2560,1811,false],"thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-150x150.jpg",150,150,true],"medium":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-300x212.jpg",300,212,true],"medium_large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-768x543.jpg",640,453,true],"large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-1024x724.jpg",640,453,true],"1536x1536":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-1536x1086.jpg",1536,1086,true],"2048x2048":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-2048x1448.jpg",2048,1448,true],"trp-custom-language-flag":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled.jpg",18,12,false],"wpsso-schema-1x1":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x1200-cropped.jpg",1200,1200,true],"wpsso-schema-4x3":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x900-cropped.jpg",1200,900,true],"wpsso-schema-16x9":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x675-cropped.jpg",1200,675,true],"wpsso-thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x628-cropped.jpg",1200,628,true],"wpsso-opengraph":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x628-cropped.jpg",1200,628,true],"wpsso-tc-summary":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x1200-cropped.jpg",1200,1200,true],"wpsso-tc-lrgimg":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/11\/BAF25-scaled-1200x628-cropped.jpg",1200,628,true]},"uagb_author_info":{"display_name":"Petra H\u016fle","author_link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/author\/hulep\/"},"uagb_comment_info":0,"uagb_excerpt":"This 5-day workshop\u00a0is\u00a0intended to give\u00a0a\u00a0thorough\u00a0introduction to Bioimage analysis\u00a0for\u00a0individuals\u00a0with little to no prior experience but who want\u00a0to\u00a0develop\u00a0some\u00a0basic\u00a0skills in image processing and analysis workflows using both open-source and proprietary software.\u00a0Participants\u00a0will\u00a0get\u00a0hands-on experience with image restoration, segmentation techniques, feature extraction and tracking using classical and advanced machine and deep learning tools. Most importantly, students will gain insight in data&hellip;","_links":{"self":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5788","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/comments?post=5788"}],"version-history":[{"count":3,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5788\/revisions"}],"predecessor-version":[{"id":5793,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5788\/revisions\/5793"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/media\/5790"}],"wp:attachment":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/media?parent=5788"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/categories?post=5788"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/tags?post=5788"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}