{"id":5693,"date":"2024-01-02T22:12:35","date_gmt":"2024-01-02T20:12:35","guid":{"rendered":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/?p=5693"},"modified":"2025-03-14T20:59:27","modified_gmt":"2025-03-14T18:59:27","slug":"bioimage-analysis-fundamentals","status":"publish","type":"post","link":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/bioimage-analysis-fundamentals\/","title":{"rendered":"BioImage Analysis Fundamentals – 2023"},"content":{"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 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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Lectors:<\/h2><\/div>\n\n\n\n
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Zuzana Burd\u00edkov\u00e1<\/span><\/h2><\/div>

burdika@natur.cuni.cz<\/a><\/p><\/div><\/div>\n\n\n\n

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Martin Sch\u00e4tz<\/span><\/h2><\/div>

schatzm@natur.cuni.cz<\/a><\/p><\/div><\/div>\n\n\n\n

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Pavel
Krist<\/span><\/h2><\/div>

pavel.krist@zeiss.com<\/a><\/p><\/div><\/div>\n\n\n\n

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Franti\u0161ek
Kitzberger<\/span><\/h2><\/div>

kitzberf@natur.cuni.cz<\/a><\/p><\/div><\/div>\n\n\n\n

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Judith Garcia Gonzales<\/span><\/h2><\/div>

garcia.judith@natur.cuni.cz<\/a><\/p><\/div><\/div>\n\n\n\n

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Paula Alejandra<\/span><\/h2><\/div>

paula.buil@ibot.cas.cz<\/a><\/p><\/div><\/div>\n\n\n\n

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For registration click here<\/a><\/div>\n<\/div>\n\n\n\n

SCHEDULE OF THE WORKSHOP<\/span><\/h2>\n\n\n

Day 1<\/strong><\/h1>\n

Basic concepts in Bioimage analysis<\/span><\/p>\n

08:45 \u2013 09:00\u00a0\u00a0\u00a0\u00a0 <\/strong>Registration<\/p>\n

09:00 \u2013 09:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Plenum: Welcome and introduction by teacher(s)<\/p>\n

09:15 \u2013 09:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Test quiz with unlimited tries<\/p>\n

09:30 \u2013 10:00\u00a0\u00a0\u00a0\u00a0 <\/strong>Introduction to Microscopy techniques<\/p>\n

10:00 \u2013 10:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Coffee break<\/p>\n

10:15 \u2013 10:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Discussion: challenges of Image acquisition and BiA<\/p>\n

10:30 \u2013 11:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to Image acquisition<\/p>\n

11:00 \u2013 11:20<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to Computer Graphic Theory<\/p>\n

11:20 \u2013 11:50<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to BiA<\/p>\n

11:50 \u2013 12:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Sum-up of the session<\/p>\n

12:00 \u2013 13:00\u00a0\u00a0\u00a0\u00a0 <\/strong>Lunch break<\/p>\n

13:00 \u2013 13:15<\/strong>\u00a0\u00a0\u00a0\u00a0 Sprint: Image preprocessing<\/p>\n

13:15 \u2013 13:30<\/strong> \u00a0\u00a0\u00a0 Discussion: where does it fit in BiA workflow?<\/p>\n

13:30 \u2013 14:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Theory: Thresholding and Segmentation (classical, ML)<\/p>\n

14:15 \u2013 14:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Coffee break<\/p>\n

14:30 \u2013 16:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Introduction to ImageJ<\/p>\n

Day 2<\/strong><\/h1>\n

Bioimage analysis using ImageJ<\/span><\/p>\n

09:00 \u2013 09:15\u00a0\u00a0\u00a0\u00a0 <\/strong>Plenum: Reflect on Day 1<\/p>\n

09:15 \u2013 09:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Discussion- Expectations for Day 2<\/p>\n

09:30 \u2013 10:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Practice BiA Workflows : Dummy Data<\/p>\n

10:30 \u2013 10:45\u00a0\u00a0\u00a0\u00a0 <\/strong>Coffee break<\/p>\n

10:45 \u2013 11:45\u00a0\u00a0\u00a0\u00a0 <\/strong>Practice BiA Workflows: Real Datasets<\/p>\n

11:45 \u2013 12:45\u00a0\u00a0\u00a0\u00a0 <\/strong>Lunch break<\/p>\n

12:45 \u2013 13:15<\/strong>\u00a0\u00a0\u00a0\u00a0 Practical Study: Intensity Based Comparison<\/p>\n

13:15 \u2013 13:45<\/strong>\u00a0\u00a0\u00a0\u00a0 Discussion: Intensity Based Comparison<\/p>\n

13:45 \u2013 14:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Coffee break<\/p>\n

14:00 \u2013 15:30<\/strong>\u00a0\u00a0\u00a0\u00a0 Practical Study: Colocalization<\/p>\n

Day 3<\/h1>\n

Bioimage analysis using Arivis\/Vision 4D<\/span><\/p>\n

09:00 \u2013 09:15<\/strong> Plenum: Reflect on Day 2<\/p>\n

09:15 \u2013 09:30<\/strong> Discussion: Expectations from Day 3<\/p>\n

09:30 \u2013 09:45<\/strong> Introduction to Arivis\/Vision 4D interface<\/p>\n

09:45 \u2013 10:45<\/strong> Practice BiA Workflows: Dummy Data<\/p>\n

10:45 \u2013 11:00<\/strong> Coffee Break<\/p>\n

11:00 \u2013 12:00<\/strong> Practice BiA Workflows: Real Datasets<\/p>\n

12:00 \u2013 13:00<\/strong> Lunch break<\/p>\n

13:00 \u2013 13:30<\/strong> Practical Study: Intensity Based Comparison<\/p>\n

13:30 \u2013 14:00<\/strong> Discussion: Intensity Based Comparison<\/p>\n

14:00 \u2013 14:15<\/strong> Coffee break<\/p>\n

14:15 \u2013 15:45<\/strong> Practical Study: Colocalization<\/p>\n

Day 4<\/strong><\/h1>\n

(Numeric) Data Analysis and Visualization \/ Final project<\/span><\/p>\n

09:00 \u2013 12:00<\/strong><\/p>\n

– Theory + Discussion: Preparing Visuals of Data Analysis<\/p>\n

– Final Project assignment<\/p>\n

– Theory + Discussion: BiA Reproducibility<\/p>\n

– Preparing Images for Protocols\/Papers – ImageJ\/ ARIVIS (?)<\/p>\n

12:00 \u2013 13:00<\/strong>\u00a0\u00a0\u00a0\u00a0 Lunch break<\/p>\n

13:00 \u2013 16:30<\/strong><\/p>\n

– Final project preparation<\/p>\n

– (Optional) AI assisted reproducible Data Science using Python, GitHub and OpenAI<\/p>\n

– (Optional) VR<\/p>\n

Day 5<\/strong><\/h1>\n

Final Project<\/span><\/p>\n

09:00 \u2013 12:00\u00a0\u00a0\u00a0\u00a0 <\/strong>Collaborative Project + presentations<\/p>\n

12:00 \u2013 13:30\u00a0\u00a0\u00a0\u00a0 <\/strong>Lunch + Goodbye<\/p>\n

Accomodation:<\/span><\/strong><\/h1>\n

We can help you arrange the accommodation.<\/p>","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":5726,"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-5693","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\/01\/poster_npo_transformace_s.jpg",1766,1398,false],"thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-150x150.jpg",150,150,true],"medium":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-300x237.jpg",300,237,true],"medium_large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-768x608.jpg",640,507,true],"large":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1024x811.jpg",640,507,true],"1536x1536":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1536x1216.jpg",1536,1216,true],"2048x2048":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s.jpg",1766,1398,false],"trp-custom-language-flag":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s.jpg",15,12,false],"wpsso-schema-1x1":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x1200-cropped.jpg",1200,1200,true],"wpsso-schema-4x3":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x900-cropped.jpg",1200,900,true],"wpsso-schema-16x9":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x675-cropped.jpg",1200,675,true],"wpsso-thumbnail":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x628-cropped.jpg",1200,628,true],"wpsso-opengraph":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x628-cropped.jpg",1200,628,true],"wpsso-tc-summary":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x1200-cropped.jpg",1200,1200,true],"wpsso-tc-lrgimg":["https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/wp-content\/uploads\/2024\/01\/poster_npo_transformace_s-1200x628-cropped.jpg",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":"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\/cs\/wp-json\/wp\/v2\/posts\/5693","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=5693"}],"version-history":[{"count":20,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts\/5693\/revisions"}],"predecessor-version":[{"id":6266,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/posts\/5693\/revisions\/6266"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/media\/5726"}],"wp:attachment":[{"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/media?parent=5693"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/categories?post=5693"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/web.natur.cuni.cz\/sekce-bi\/VMCF\/cs\/wp-json\/wp\/v2\/tags?post=5693"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}