Difference between revisions of "Image Processing School Pilsen 2009"

(reorder entries according to the current schedule)
(removed image acquisition)
Line 18: Line 18:
 
|Session 2: 11:30 - 12:30
 
|Session 2: 11:30 - 12:30
 
|[[#Image Processing fundamentals|Image Processing Fundamentals]]
 
|[[#Image Processing fundamentals|Image Processing Fundamentals]]
|[[#Fiji scripting: Python|Fiji scripting: Python]]
+
|
 
|[[#Beyond 3D|Beyond 3D]]
 
|[[#Beyond 3D|Beyond 3D]]
 
|
 
|
 
|-
 
|-
 
|Session 3: 14:00 - 15:30
 
|Session 3: 14:00 - 15:30
|[[#Fundamentals of image acquisition|Fundamentals of image acquisition ]]
+
|[[#Fiji scripting: Python|Fiji scripting: Python]]
 
|[[#TrakEM2|TrakEM2]]
 
|[[#TrakEM2|TrakEM2]]
 
|[[#Fiji scripting: advanced Python|Fiji scripting: advanced Python]]
 
|[[#Fiji scripting: advanced Python|Fiji scripting: advanced Python]]
Line 49: Line 49:
 
=== Image Processing fundamentals ===
 
=== Image Processing fundamentals ===
  
Fundamentals of image processing: anatomy of a digital image, image formats
+
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]]
 
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 ==
 
== Thursday ==

Revision as of 04:12, 1 September 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 Segmentation Registration
Session 2: 11:30 - 12:30 Image Processing Fundamentals 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

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

Thursday

Measurements

Image analysis: measurements

Lead instructor: Dan White

Colocalization

Image analysis: Colocalization

Lead instructor: Dan White

Fiji scripting: Python

Introduction to Fiji scripting in Python

Lead instructor: Johannes Schindelin

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: Virtual Stack Slice Registration, TrakEM2, bUnwarpJ

Lead instructor: Ignacio Arganda

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.