Basic image analysis: focused on microscopy applications - 2 ECTS
Course dates: 7-11 October 2013
Preferred number of students: <30
Lecturers: Ida-Maria Sintorn (main lecturer), Cris Luengo and/or Carolina Wählby
Place: Naturvetarhuset, room Na230 and Na220
Registration is closed.


Main learning objectives:
To understand basic concepts and methods in computerized image analysis
To become familiar with image analysis software
To be able to choose and apply suitable image analysis methods to extract quantitative information from images in real applications

Equipment: student’s own laptops

Examination: Short report with analysis approach, implementation, and conclusion on own problem.

Preliminary schedule:

Monday
13-15 Introduction: what is image analysis and how is it used, basic concepts
15-17 Digitization & fundamental techniques: image formation process, image types, pixels, histogram, contrast/brightness

Tuesday
8-10 Preprocessing: spatial and frequency filtering, noise removal, background subtraction
10-12 Segmentation: thresholding, region based methods, matching
13-17 Computer exercise: ImageJ or Fiji

Wednesday
8-10 Object representation: shape simplification, skeletonization
10-12 Quantitative measures: stereology, accuracy, precision, bias
13-17 Seminar/group exercise: own problems

Thursday
8-10 Quantitative measurements: evaluation, ground truth
10-12 Feature extraction: intensity, shape and texture measures
13-17 Computer exercise: CellProfiler & CellProfiler Analyst

Friday
8-10 Classification: basic theory, ML classifiers, decision trees, clustering
10-12 Summary