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.

SCHEDULE OF THE WORKSHOP

Day 1: Introduction to Microscopy and Bioimage Analysis

09:00 – 09:15 Introduction

09:15 – 09:30 Test Quiz

09:30 – 10:00 Introduction to Microscopy Techniques

10:00 – 10:15 Coffee break

10:15 – 10:50 Discussion: Challenges in Image Acquisition and Bioimage Analysis

10:50 – 11:20 Introduction to Image Acquisition

11:20 – 11:40 Introduction to Image Preprocessing

11:45 – 12:10 Image Preprocessing – work in groups

12:10 – 13:10 Lunch break

13:10 – 13:40 Introduction to Bioimage Analysis

13:40 – 14:10 Discussion on bioimage analysis and image preprocessing

14:10 – 15:05 Threshold and Segmentation: lecture and work in groups

15:05 – 15:20 Coffee break

15:20 – 15:30 Brief Introduction to ImageJ

Day 2: ImageJ

09:30 – 09:40 Plenum: Reflect on Day 1

09:40 – 09:50 Discussion: Expectations for Day 2

09:50 – 10:15 Introduction to ImageJ

10:15 – 10:30 Coffee break

10:30 – 11:45 Practice BiA Workflows: getting to know ImageJ (basic image functions, segmentation pipelines, GPU-accelerated image analysis)

11:45 – 12:45 Lunch break

12:45 – 13:45 Practice BiA Workflows: Intensity-Based Comparisons (image preprocessing and intensity quantification)

13:45 – 14:00 Coffee break

14:00 – 15:30 Practice BiA Workflows: Image stitching

14:00 – 15:30 Practice BiA Workflows: Pixel-based Colocalization

Day 3: ARIVIS

09:30 – 09:40 Plenum: Reflect on Day 2

09:45 – 10:00 Discussion: Expectations for Day3

10:00 – 10:30 Introduction to ARIVIS user interface

10:30 – 10:50 Coffee break

10:50 – 12:00 Practice BiA Workflows: Data import, 3D visualization, segmentation

12:00 – 13:00 Lunch break

13:00 – 14:00 Practice BiA Workflows: ML segmentation, Cellpose in ARIVIS

14:00 – 14:15 Coffee break

14:15 – 15:15 Practice BiA Workflows: colocalization and tracking

Day 4: Data visualization / Final project preparation

09:00 – 09:15 Reflection on Day 3

09:15 – 10:15 Preparing Visuals of Data Analysis & Introduction to Reproducible Data Science in Practice

10:30 – 11:15 Final project preparation

11:50 – 13:15 Lunch break

Coffee break – in between sessions/when needed

Day 5: Final projects

09:00 Projects finalization, upload and presentations

Coffee break – in between sessions/when needed