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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.