Difference between revisions of "Image Processing School Pilsen 2009"

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|[[#Measurements|Measurements]] and [[#Colocalization|Colocalization]]
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|[[#Fundamentals of image acquisition|Fundamentals of image acquisition ]]
 
|[[#Fundamentals of image acquisition|Fundamentals of image acquisition ]]
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Revision as of 12:41, 31 August 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 Measurements and Colocalization Beyond 3D Segmentation
Session 2: 11:30 - 12:30 Image Processing Fundamentals Fiji scripting: Python Registration
Session 3: 14:00 - 15:30 Fundamentals of image acquisition TrakEM2 Fiji scripting: advanced Python
Session 4: 16:00 - 17:30 Show your images! Work session Work session

Wednesday

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

Lead instructor: Albert Cardona

Fundamentals of image acquisition

Fundamentals of image acquisition: effects of dynamic range and exposure, etc

Lead instructor: Albert Cardona or ?

Thursday

Measurements

Image analysis: measurements

Lead instructor: Dan White

Fiji scripting: Python

Introduction to Fiji scripting in Python

Lead instructor: Johannes Schindelin

Colocalization

Image analysis: Colocalization

Lead instructor: Dan White

Friday

Beyond 3D

Intensity vs time analysis

Lead instructor: Jean-Yves Tinevez

Registration

Image registration: Virtual Stack Slice Registration, TrakEM2, bUnwarpJ

Lead instructor: Ignacio Arganda

Fiji scripting: advanced Python

Advanced Fiji scripting in Python

Lead instructors: Jean-Yves Tinevez

Saturday

TrakEM2

TrakEM2: image registration and manual segmentation.

Lead instructor: Albert Cardona

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

Writing Fiji plugins in Java

Introduction to Fiji programming in Java

Lead instructor: Johannes Schindelin

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.