{"id":7040,"date":"2026-04-23T13:42:44","date_gmt":"2026-04-23T11:42:44","guid":{"rendered":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=7040"},"modified":"2026-04-23T13:16:04","modified_gmt":"2026-04-23T11:16:04","slug":"fundamentals-of-bioimage-analysis-may-26","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/fundamentals-of-bioimage-analysis-may-26\/","title":{"rendered":"Fundamentals of bioimage analysis \u2013 May 26"},"content":{"rendered":"<div class=\"wp-block-image is-style-default\">\n<figure class=\"aligncenter size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"724\" height=\"1024\" src=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-724x1024.png\" alt=\"\" class=\"wp-image-7041\" srcset=\"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-724x1024.png 724w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-1086x1536.png 1086w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-8x12.png 8w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-212x300.png 212w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer-768x1086.png 768w, https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2026\/04\/2026_NPO_Flyer.png 1414w\" sizes=\"auto, (max-width: 724px) 100vw, 724px\" \/><\/figure>\n<\/div>\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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\u2019ll learn how to create reproducible data visualizations and manage your bioimage data effectively.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Upon successful completion of the course, participants will be awarded a digital microcertificate, aligning with the unified European framework.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>What will you learn?<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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<p class=\"wp-block-paragraph\"><strong>Workshop Agenda<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><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 class=\"wp-block-paragraph\"><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 class=\"wp-block-paragraph\"><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 class=\"wp-block-paragraph\"><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 class=\"wp-block-paragraph\"><strong>Registration and Fees<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>For Registration, click here:<\/strong>&nbsp;<a href=\"https:\/\/is.cuni.cz\/studium\/prijimacky\/index.php?do=detail_kurz_mc&amp;cid=12870\">Registration link<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">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>&nbsp;2956 K\u010d<\/li>\n\n\n\n<li><strong>Fee for a Charles University student:<\/strong>\u00a0541 K\u010d<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","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":6,"featured_media":0,"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-7040","post","type-post","status-publish","format-standard","hentry","category-courses","category-workshops"],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"trp-custom-language-flag":false,"wpsso-schema-1x1":false,"wpsso-schema-4x3":false,"wpsso-schema-16x9":false,"wpsso-thumbnail":false,"wpsso-opengraph":false,"wpsso-tc-summary":false,"wpsso-tc-lrgimg":false},"uagb_author_info":{"display_name":"Martin Sch\u00e4tz","author_link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/author\/schatzm\/"},"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\/wp-json\/wp\/v2\/posts\/7040","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\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/comments?post=7040"}],"version-history":[{"count":3,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/7040\/revisions"}],"predecessor-version":[{"id":7044,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/7040\/revisions\/7044"}],"wp:attachment":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/media?parent=7040"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/categories?post=7040"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/tags?post=7040"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}