{"id":5757,"date":"2024-06-26T10:14:54","date_gmt":"2024-06-26T08:14:54","guid":{"rendered":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=5757"},"modified":"2025-03-14T20:59:26","modified_gmt":"2025-03-14T18:59:26","slug":"bioimage-analysis-fundamentals-2","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/bioimage-analysis-fundamentals-2\/","title":{"rendered":"BioImage Analysis Fundamentals – 2024"},"content":{"rendered":"\n

Welcome to our BioImage Analysis Fundamentals workshop! Dive into the world of bioimage analysis and discover the power of tools like ImageJ and Arivis\/Vision4D for image processing and evaluation. Explore the possibilities of machine learning and deep learning in interpreting microscopy data. Learn to visualize your findings effectively for impactful research. Join us on the exciting journey of unlocking the secrets hidden within microscopic images! By the end of this 5-day workshop, you will have a solid skillset to effectively analyze, visualize and interpret your own bioimage data.<\/p>\n\n\n\n

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FOR REGISTRATION CLICK HERE<\/div><\/a><\/div><\/div>\n<\/div><\/div>\n\n\n\n

SCHEDULE OF THE WORKSHOP<\/strong><\/span><\/p>\n\n\n\n

Day 1: Introduction to Microscopy and Bioimage Analysis<\/h1>\n\n\n\n

09:00 \u2013 09:15 Introduction<\/p>\n\n\n\n

09:15 \u2013 09:30 Test Quiz<\/p>\n\n\n\n

09:30 \u2013 10:00 Introduction to Microscopy Techniques<\/p>\n\n\n\n

10:00 \u2013 10:15 Coffee break<\/strong><\/p>\n\n\n\n

10:15 \u2013 10:50 Discussion: Challenges in Image Acquisition and Bioimage Analysis<\/p>\n\n\n\n

10:50 \u2013 11:20 Introduction to Image Acquisition<\/p>\n\n\n\n

11:20 \u2013 11:40 Introduction to Image Preprocessing<\/p>\n\n\n\n

11:45 \u2013 12:10 Image Preprocessing – work in groups<\/p>\n\n\n\n

12:10 \u2013 13:10 Lunch break<\/strong><\/p>\n\n\n\n

13:10 \u2013 13:40 Introduction to Bioimage Analysis<\/p>\n\n\n\n

13:40 \u2013 14:10 Discussion on bioimage analysis and image preprocessing<\/p>\n\n\n\n

14:10 \u2013 15:05 Threshold and Segmentation: lecture and work in groups<\/p>\n\n\n\n

15:05 \u2013 15:20 Coffee break<\/strong><\/p>\n\n\n\n

15:20 \u2013 15:30 Brief Introduction to ImageJ<\/p>\n\n\n\n

Day 2: ImageJ<\/h1>\n\n\n\n

09:30 \u2013 09:40 Plenum: Reflect on Day 1<\/p>\n\n\n\n

09:40 \u2013 09:50 Discussion: Expectations for Day 2<\/p>\n\n\n\n

09:50 \u2013 10:15 Introduction to ImageJ<\/p>\n\n\n\n

10:15 \u2013 10:30 Coffee break<\/strong><\/p>\n\n\n\n

10:30 \u2013 11:45 Practice BiA Workflows: getting to know ImageJ (basic image functions, segmentation pipelines, GPU-accelerated image analysis)<\/p>\n\n\n\n

11:45 \u2013 12:45 Lunch break<\/strong><\/p>\n\n\n\n

12:45 \u2013 13:45 Practice BiA Workflows: Intensity-Based Comparisons (image preprocessing and intensity quantification)<\/p>\n\n\n\n

13:45 \u2013 14:00 Coffee break<\/strong><\/p>\n\n\n\n

14:00 \u2013 15:30 Practice BiA Workflows: Image stitching<\/p>\n\n\n\n

14:00 \u2013 15:30 Practice BiA Workflows: Pixel-based Colocalization<\/p>\n\n\n\n

Day 3: ARIVIS<\/h1>\n\n\n\n

09:30 \u2013 09:40 Plenum: Reflect on Day 2<\/p>\n\n\n\n

09:45 \u2013 10:00 Discussion: Expectations for Day3<\/p>\n\n\n\n

10:00 – 10:30 Introduction to ARIVIS user interface<\/p>\n\n\n\n

10:30 \u2013 10:50 Coffee break<\/strong><\/p>\n\n\n\n

10:50 \u2013 12:00 Practice BiA Workflows: Data import, 3D visualization, segmentation<\/p>\n\n\n\n

12:00 – 13:00 Lunch break<\/strong><\/p>\n\n\n\n

13:00 – 14:00 Practice BiA Workflows: ML segmentation, Cellpose in ARIVIS<\/p>\n\n\n\n

14:00 – 14:15 Coffee break<\/strong><\/p>\n\n\n\n

14:15 – 15:15 Practice BiA Workflows: colocalization and tracking<\/p>\n\n\n\n

Day 4: Data visualization \/ Final project preparation<\/h1>\n\n\n\n

09:00 \u2013 09:15 Reflection on Day 3<\/p>\n\n\n\n

09:15 \u2013 10:15 Preparing Visuals of Data Analysis & Introduction to Reproducible Data Science in Practice<\/p>\n\n\n\n

10:30 – 11:15 Final project preparation<\/p>\n\n\n\n

11:50 \u2013 13:15 Lunch break<\/strong><\/p>\n\n\n\n

Coffee break<\/strong> – in between sessions\/when needed<\/p>\n\n\n\n

Day 5: Final projects<\/h1>\n\n\n\n

09:00 Projects finalization, upload and presentations<\/p>\n\n\n\n

Coffee break<\/strong> – in between sessions\/when needed<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

Welcome to our BioImage Analysis Fundamentals workshop! Dive into the world of bioimage analysis and discover the power of tools like ImageJ and Arivis\/Vision4D for image processing and evaluation. Explore the possibilities of machine learning and deep learning in interpreting microscopy data. Learn to visualize your findings effectively for impactful research. Join us on the […]<\/p>\n","protected":false},"author":3,"featured_media":5765,"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-5757","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\/06\/02.jpg",723,703,false],"thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02-150x150.jpg",150,150,true],"medium":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02-300x292.jpg",300,292,true],"medium_large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",640,622,false],"large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",640,622,false],"1536x1536":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"2048x2048":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"trp-custom-language-flag":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",12,12,false],"wpsso-schema-1x1":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-schema-4x3":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-schema-16x9":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-opengraph":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-tc-summary":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false],"wpsso-tc-lrgimg":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/06\/02.jpg",723,703,false]},"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":"Welcome to our BioImage Analysis Fundamentals workshop! Dive into the world of bioimage analysis and discover the power of tools like ImageJ and Arivis\/Vision4D for image processing and evaluation. Explore the possibilities of machine learning and deep learning in interpreting microscopy data. Learn to visualize your findings effectively for impactful research. Join us on the…","_links":{"self":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5757","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=5757"}],"version-history":[{"count":7,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5757\/revisions"}],"predecessor-version":[{"id":6265,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/posts\/5757\/revisions\/6265"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/media\/5765"}],"wp:attachment":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/media?parent=5757"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/categories?post=5757"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-json\/wp\/v2\/tags?post=5757"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}