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See also the Image Processing School announcement webpage.
Schedule (tentative):
| Time | Wednesday, September 9th | Thursday, September 10th | Friday, September 11th | Saturday, September 12th |
|---|---|---|---|---|
| Session 1: 9:30 - 11:00 | Welcome and Installing Fiji | Quantitative Imaging | Segmentation | Registration |
| Session 2: 11:30 - 12:30 | Image Processing Fundamentals | Colocalization | Beyond 3D | |
| Session 3: 14:00 - 15:30 | Fiji scripting: Python | TrakEM2 | Fiji scripting: advanced Python | |
| Session 4: 16:00 - 17:30 | Show your images! | Work session | Work session |
Wednesday
Welcome and Introduction
Overview of installing and using Fiji
Setup: installing Fiji and getting familiar with it; overview of major features.
Lead instructor: Johannes Schindelin
Image Processing fundamentals
Fundamentals of image processing: anatomy of a digital image, image formats. Includes notes on image acquisition (effects of dynamic range and exposure times)
Lead instructor: Albert Cardona
Fiji scripting: Python
Introduction to Fiji scripting in Python
Lead instructor: Johannes Schindelin
Thursday
Quantitative Imaging
Quantitative image acquisition and analysis: Spectroscopy not photography, simple measurements.
The presentation is available online (PDF) here!
Lead instructor: Dan White
Colocalization
Quantitative Image analysis: What you need to know about Colocalization Analysis
The presentation is available online (PDF) here!
Lead instructor: Dan White
TrakEM2
TrakEM2: image registration and manual segmentation.
Lead instructor: Albert Cardona
Friday
Segmentation
Introduction to image segmentation.
- Pixel-based and vector-based.
- Manual and semi-automatic.
Plugins: Simple Neurite Tracer, Segmentation Editor, VIB protocol, TrakEM2, Level Sets.
Lead instructor: Verena Kaynig
Beyond 3D
Intensity vs time analysis
Lead instructor: Jean-Yves Tinevez
Fiji scripting: advanced Python
Advanced Fiji scripting in Python
Lead instructors: Jean-Yves Tinevez
Writing Fiji plugins in Java
Introduction to Fiji programming in Java (this will be an add-on to the advanced scripting).
Lead instructor: Johannes Schindelin
Saturday
Registration
Image registration: rigid, affine, elastic, maximal warping… (Register Virtual Stack Slices, TrakEM2, BUnwarpJ)
Lead instructor: Ignacio Arganda-Carreras
Work sessions
At the end of every day, there is time to apply what you learnt and go beyond that. You can process your own images and discuss results and methods with the instructors.
