DIPP predoc course Freemat/Matlab

DIPP Predoc course Freemat/Matlab

This one-week practical teaches basic programming in Matlab/Freemat. We use the free open-source clone Freemat, but the syntax and language are identical with those of the commercial product Matlab and the free clone Octave. The practical focuses on basic bio-image data analysis and post-processing. This course is part of the DIPP/IMPRS graduate training.


Contents

Introduction to programming, installing Freemat, basic Freemat/Matlab primer, analysis of biological image data using Freemat/Matlab.


Learning goals
  • Understand the procedural/array programming paradigm of Matlab/Freemat/Octave

  • Be able to write own scripts and functions

  • Use array operations and control structures to do basic image processing

Special remarks

We focus on biological image analysis. The taught methods and concepts are, however, applicable in a much broader sense, and the internet is a rich resource of additional primers and documentation.


Course language: ENGLISH


Please find below the course syllabus:
  • Day 1: Introduction, Installation of software, work though the primer
  • Days 2-4: Practical project work in groups on biological image analysis
  • Day 5: wrap-up and report writing
Project

The practical project will aim at implementing a program that segments a cell from a DIC image, detects fluorescent virus particles in another image, and plots the virus-to-nucleus distance distribution as a function of time post infection. Raw images were kindly provided by the group of Urs Greber, University of Zurich, Switzerland.


Tutors
  • Yuanhao Gong (MOSAIC Group, MPI-CBG)
  • Ulrik Guenther (TUD Physics)