{"id":5817,"date":"2025-03-11T20:36:12","date_gmt":"2025-03-11T18:36:12","guid":{"rendered":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=5817"},"modified":"2025-04-01T20:11:08","modified_gmt":"2025-04-01T18:11:08","slug":"fundamentals-of-bioimage-analysis-june-25","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/fundamentals-of-bioimage-analysis-june-25\/","title":{"rendered":"Z\u00e1klady bioimage anal\u00fdzy \u2013 25. \u010dervna"},"content":{"rendered":"<h2 class=\"wp-block-heading\"><strong>Overview<\/strong><\/h2>\n\n\n\n<p>This 5-day workshop is designed to provide a thorough introduction to bioimage analysis for individuals with little to no prior experience. Participants will develop essential skills in image processing and analysis workflows using both open-source and proprietary software, namely Fiji\/ImageJ and Arivis. Through hands-on sessions, you\u2019ll explore techniques for image restoration, segmentation, feature extraction, and tracking\u2014employing both classical methods and cutting-edge machine and deep learning tools. Most importantly, you&#8217;ll learn how to create reproducible data visualizations and manage your bioimage data effectively.<\/p>\n\n\n\n<p>Upon successful completion of the course, participants will be awarded a digital microcertificate, aligning with the unified European framework.<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"724\" height=\"1024\" src=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-724x1024.png\" alt=\"\" class=\"wp-image-6520\" style=\"width:840px;height:auto\" srcset=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-724x1024.png 724w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-212x300.png 212w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-768x1086.png 768w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-1086x1536.png 1086w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer-8x12.png 8w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer.png 1414w\" sizes=\"auto, (max-width: 724px) 100vw, 724px\" \/><\/figure>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-9d6595d7 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\" style=\"flex-basis:100%\">\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-7b82f5dc\"><div class=\"uagb-buttons__wrap uagb-buttons-layout-wrap\">\n<div class=\"wp-block-uagb-buttons-child uagb-buttons__outer-wrap uagb-block-3dcb20fe wp-block-button\"><div class=\"uagb-button__wrapper\"><a class=\"uagb-buttons-repeater wp-block-button__link\" aria-label=\"\" href=\"https:\/\/is.cuni.cz\/studium\/eng\/prijimacky\/index.php?do=detail_kurz_mc&amp;cid=11201\" rel=\"follow noopener\" target=\"_blank\" role=\"button\"><div class=\"uagb-button__link\">SIS REGISTRATION CLICK HERE (EN)<\/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\n\n\n<div class=\"wp-block-uagb-buttons-child uagb-buttons__outer-wrap uagb-block-e96bfb0a wp-block-button\"><div class=\"uagb-button__wrapper\"><a class=\"uagb-buttons-repeater wp-block-button__link\" aria-label=\"\" href=\"https:\/\/is.cuni.cz\/studium\/prijimacky\/index.php?do=detail_kurz_mc&amp;cid=11201\" rel=\"follow noopener\" target=\"_blank\" role=\"button\"><div class=\"uagb-button__link\">SIS REGISTRACE ZDE (CZ) <\/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<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>What will you learn?<\/strong><\/h2>\n\n\n\n<p>By the end of this workshop, you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Understand Foundational Microscopy Techniques<\/strong><br>Gain insights into the principles of bioimage acquisition and analysis.<\/li>\n\n\n\n<li><strong>Apply Essential Image Processing Methods<\/strong><br>Use thresholding, segmentation, and preprocessing techniques to analyze bioimages.<\/li>\n\n\n\n<li><strong>Utilize Leading Software Tools<\/strong><br>Master FIJI\/ImageJ for detailed analyses such as stitching, colocalization, and intensity comparisons; leverage ZEISS arivis for advanced 3D visualization, ML-based segmentation, and tracking.<\/li>\n\n\n\n<li><strong>Develop Reproducible Workflows<\/strong><br>Create consistent and reproducible data visualizations and analysis pipelines.<\/li>\n\n\n\n<li><strong>Engage in Real-World Projects<\/strong><br>Work on a final project to apply your newly acquired skills to an authentic bioimage analysis challenge.<\/li>\n\n\n\n<li><strong>Collaborate and Network<\/strong><br>Connect with peers and experts to foster professional relationships and knowledge exchange.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Workshop Agenda<\/strong><\/h2>\n\n\n\n<p><strong>Day 1: Introduction to Microscopy and Bioimage Analysis<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Workshop Introduction and Overview<\/li>\n\n\n\n<li>Microscopy Techniques: Principles, types, and applications<\/li>\n\n\n\n<li>Image Acquisition: Methods and challenges<\/li>\n\n\n\n<li>Image Preprocessing: Practical group exercises<\/li>\n\n\n\n<li>Introduction to Thresholding and Segmentation<\/li>\n\n\n\n<li>Partner lecture : Autonomous Microscopy Powered by AIVIA<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 2: FIJI\/ImageJ<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Overview of the FIJI\/ImageJ Interface and Key Functions<\/li>\n\n\n\n<li>Hands-On Practice: Basic analysis workflows including segmentation and GPU-accelerated tools<\/li>\n\n\n\n<li>Advanced Processing: Image stitching, intensity quantification, and pixel-based colocalization<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 3: ZEISS arivis<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Getting Started with ARIVIS: User interface, data import, and setup<\/li>\n\n\n\n<li>3D Visualization and Segmentation: Hands-on practice<\/li>\n\n\n\n<li>Machine Learning in ARIVIS: Using 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><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Creating Effective Visualizations for Data Analysis<\/li>\n\n\n\n<li>Introduction to Reproducible Science: Best practices for consistent workflows<\/li>\n\n\n\n<li>Project Work: Setting up your final project and defining objectives<\/li>\n<\/ul>\n\n\n\n<p><strong>Day 5: Final Projects and Presentations<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Final Project Work: Implementation, refinement, and preparation<\/li>\n\n\n\n<li>Project Presentations: Sharing your solutions to real-world bioimage challenges<\/li>\n<\/ul>\n\n\n\n<p><em>Note: Refreshments are included in the price of the workshop.<\/em><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Registration and Fees<\/strong><\/h2>\n\n\n\n<p><strong>For Registration, click here:<\/strong> <a href=\"https:\/\/is.cuni.cz\/studium\/eng\/prijimacky\/index.php?do=detail_kurz_mc&amp;cid=11201\">Registration link<\/a><\/p>\n\n\n\n<p>We offer tiered registration fees for:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Fee for a continuing education (C\u017dV) participant:<\/strong> 3576.76 K\u010d (incl. DPH)<\/li>\n\n\n\n<li><strong>Fee for a Charles University student or \u201csubsidized participant\u201d:<\/strong> 492 K\u010d (not subject to DPH)<\/li>\n\n\n\n<li><strong>Additional fee for a Charles University student*:<\/strong> 541.30 K\u010d (not subject to DPH)<\/li>\n<\/ul>\n\n\n\n<p>* The additional fee for a Charles University student applies when a student enrolled in the course as part of their accredited study program (i.e., an elective) and later decides they also want an official C\u017dV certificate. Because the student\u2019s primary tuition is already covered through standard university funding, this extra fee covers the administrative and certification costs specifically related to issuing the continuing education (C\u017dV) certificate.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Preparation and Additional Resources<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Computers &amp; Software:<\/strong> Computers and the required software will be provided for the workshop.<\/li>\n\n\n\n<li><strong>Materials &amp; Datasets:<\/strong> All required datasets and course materials will be shared prior to the workshop.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Questions?<\/strong><\/h2>\n\n\n\n<p>For further inquiries or more information, please fill the <a href=\"https:\/\/forms.gle\/PkVB644H4nWUvtHL6\">contact form<\/a><\/p>\n\n\n\n<p><\/p>","protected":false},"excerpt":{"rendered":"<p>Overview This 5-day workshop is designed to provide a thorough introduction to bioimage analysis for individuals with little to no prior experience. Participants will develop essential skills in image processing and analysis workflows using both open-source and proprietary software, namely Fiji\/ImageJ and Arivis. Through hands-on sessions, you\u2019ll explore techniques for image restoration, segmentation, feature extraction, [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":6522,"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-5817","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\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI.png",4963,3591,false],"thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-150x150.png",150,150,true],"medium":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-300x217.png",300,217,true],"medium_large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-768x556.png",640,463,true],"large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1024x741.png",640,463,true],"1536x1536":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1536x1111.png",1536,1111,true],"2048x2048":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-2048x1482.png",2048,1482,true],"trp-custom-language-flag":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-18x12.png",18,12,true],"wpsso-schema-1x1":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x1200-cropped.png",1200,1200,true],"wpsso-schema-4x3":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x900-cropped.png",1200,900,true],"wpsso-schema-16x9":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x675-cropped.png",1200,675,true],"wpsso-thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x628-cropped.png",1200,628,true],"wpsso-opengraph":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x628-cropped.png",1200,628,true],"wpsso-tc-summary":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x1200-cropped.png",1200,1200,true],"wpsso-tc-lrgimg":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2025\/03\/Image-Analysis-fundamentals_June-2025_flyer_MINI-1200x628-cropped.png",1200,628,true]},"uagb_author_info":{"display_name":"Petra H\u016fle","author_link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/author\/hulep\/"},"uagb_comment_info":0,"uagb_excerpt":"Overview This 5-day workshop is designed to provide a thorough introduction to bioimage analysis for individuals with little to no prior experience. Participants will develop essential skills in image processing and analysis workflows using both open-source and proprietary software, namely Fiji\/ImageJ and Arivis. Through hands-on sessions, you\u2019ll explore techniques for image restoration, segmentation, feature extraction,&hellip;","_links":{"self":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts\/5817","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/comments?post=5817"}],"version-history":[{"count":6,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts\/5817\/revisions"}],"predecessor-version":[{"id":6525,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts\/5817\/revisions\/6525"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/media\/6522"}],"wp:attachment":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/media?parent=5817"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/categories?post=5817"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/tags?post=5817"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}