Original draft program

Initial draft written by Marina. Please don’t edit this page (for now). Keeping it here as a reference.

The current program is here.

πŸ“… Day 1 – Introduction to Light-Sheet and 3D Visualization

🧠 Morning Session
- Welcome & Course Overview
- Principles of Light-Sheet Microscopy
- Optical setup & acquisition strategies
- Experiment planning and sample mounting
- Common image artifacts and how to avoid/fix them
- Introduction to light-sheet datasets: file types, metadata, scale, volume/time complexity

πŸ–₯️ Afternoon Workshop
- Multiview reconstruction in Fiji
- Hands-on with 3D visualization in Fiji and Napari

πŸ“… Day 2 – Image Analysis Fundamentals

🧠 Morning Session
- Fundamentals of BioImage Analysis
- Image types and bit depth
- Noise, background correction, filters
- Thresholding, segmentation basics (pixel vs object)
- ROI handling and masks
- Overview of available open-source tools

πŸ–₯️ Afternoon Workshop
- Segmentation workflows in Fiji and Napari (2D/3D)
- Intro to cell tracking methods

πŸ“… Day 3 – Machine Learning and AI for Image Analysis

🧠 Morning Session
- Introduction to AI and deep learning in microscopy
- When and why to use DL models
- Overview of StarDist, CellPose

πŸ–₯️ Afternoon Workshop
- Using BioImage Model Zoo models with Napari
- Hands-on with Labkit and ilastik (interactive annotation & classification)
- Deploying pre-trained models on user data
- Optional: Train your own simple model (time permitting)

πŸ“… Day 4 – Applications & Independent Project Work

🧠 Morning Session
- Research applications of BioImage Analysis
- Talks or case studies using light-sheet imaging
- Highlight multi-disciplinary projects (e.g. developmental biology, neuroscience, plant science)
- Tips for designing an effective analysis pipeline

πŸ–₯️ Afternoon Workshop
- Begin working on personal projects or example datasets
- Q&A with instructors (project clinic)
- Begin structuring project presentations (suggested format below)

πŸ“… Day 5 – Final Projects & Presentations

🧠 Morning Session
- Continue work on projects
- Finalize analysis and prepare presentations
- Instructor support for polishing visuals and conclusions

πŸ–₯️ Afternoon Session
- Student Presentations (10 min each + 5 min Q&A)
- Suggested format:
1. Dataset and biological question
2. Analysis goal
3. Method and tools used
4. Results
5. Challenges & next steps
- Group Discussion and Feedback
- Closing Remarks & Certificate Distribution
- Group Dinner πŸŽ‰