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

Basic concepts in Bioimage analysis

08:45 – 09:00     Registration

09:00 – 09:15     Plenum: Welcome and introduction by teacher(s)

09:15 – 09:30     Test quiz with unlimited tries

09:30 – 10:00     Introduction to Microscopy techniques

10:00 – 10:15     Coffee break

10:15 – 10:30     Discussion: challenges of Image acquisition and BiA

10:30 – 11:00     Introduction to Image acquisition

11:00 – 11:20     Introduction to Computer Graphic Theory

11:20 – 11:50     Introduction to BiA

11:50 – 12:00     Sum-up of the session

12:00 – 13:00     Lunch break

13:00 – 13:15     Sprint: Image preprocessing

13:15 – 13:30     Discussion: where does it fit in BiA workflow?

13:30 – 14:15     Theory: Thresholding and Segmentation (classical, ML)

14:15 – 14:30     Coffee break

14:30 – 16:00     Introduction to ImageJ

Day 2

Bioimage analysis using ImageJ

09:00 – 09:15     Plenum: Reflect on Day 1

09:15 – 09:30     Discussion- Expectations for Day 2

09:30 – 10:30     Practice BiA Workflows : Dummy Data

10:30 – 10:45     Coffee break

10:45 – 11:45     Practice BiA Workflows: Real Datasets

11:45 – 12:45     Lunch break

12:45 – 13:15     Practical Study: Intensity Based Comparison

13:15 – 13:45     Discussion: Intensity Based Comparison

13:45 – 14:00     Coffee break

14:00 – 15:30     Practical Study: Colocalization

Day 3

Bioimage analysis using Arivis/Vision 4D

09:00 – 09:15 Plenum: Reflect on Day 2

09:15 – 09:30 Discussion: Expectations from Day 3

09:30 – 09:45 Introduction to Arivis/Vision 4D interface

09:45 – 10:45 Practice BiA Workflows: Dummy Data

10:45 – 11:00 Coffee Break

11:00 – 12:00 Practice BiA Workflows: Real Datasets

12:00 – 13:00 Lunch break

13:00 – 13:30 Practical Study: Intensity Based Comparison

13:30 – 14:00 Discussion: Intensity Based Comparison

14:00 – 14:15 Coffee break

14:15 – 15:45 Practical Study: Colocalization

Day 4

(Numeric) Data Analysis and Visualization / Final project

09:00 – 12:00

– Theory + Discussion: Preparing Visuals of Data Analysis

– Final Project assignment

– Theory + Discussion: BiA Reproducibility

– Preparing Images for Protocols/Papers – ImageJ/ ARIVIS (?)

12:00 – 13:00     Lunch break

13:00 – 16:30

– Final project preparation

– (Optional) AI assisted reproducible Data Science using Python, GitHub and OpenAI

– (Optional) VR

Day 5

Final Project

09:00 – 12:00     Collaborative Project + presentations

12:00 – 13:30     Lunch + Goodbye

Accomodation:

We can help you arrange the accommodation.