This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at

Image Processing School Pilsen 2009

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


Welcome and Introduction

Albert Cardona

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


Quantitative Imaging

Quantitative image acquisition and analysis: Spectroscopy not photography, simple measurements.

The presentation is available online (PDF) here!

Lead instructor: Dan White


Quantitative Image analysis: What you need to know about Colocalization Analysis

The presentation is available online (PDF) here!

Lead instructor: Dan White


TrakEM2: image registration and manual segmentation.

Lead instructor: Albert Cardona



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



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.