Handouts

Date Title Description
Lecture 1 (January 10, 2011; Week 1) Introduction  
Lecture 2 (Jaunary 12, 2011; Week 1)

Fundamentals of light microscopy

  
Lecture 3 (January 19, 2011; Week 2) Practical issues in bioimage informatics

READING assignment 1 handout

Peng et al review; Swedlow et al review 1; Swedlow et al review 2; Danuser review; Peperkok et al review
Lecture 4 (January 26, 2011; Week 3)

Fundamentals of fluorescence microscopy

  
Lecture 5 (January 31, 2011; Week 4) Fundamentals of fluorescence microscopy (continued); Bioimage data analysis (I): Overview

PROJECT assignment 1 handout
Lecture 6 (February 02, 2011; Week 4) Bioimage data analysis (II): Image alignment/registration

Zitova&Flusser; Maintz&Viergever; Baker&Matthews
Lecture 7 (February 07, 2011; Week 5) Bioimage data analysis (II): Image alignment/registration; (III): Point feature detection, Part I

Reading assignment 2 handout

 

Lecture 8 (February 09, 2011; Week 5)

 Bioimage data analysis (III): Point feature detection, Part I & II

Cheezum et al; Yildiz&Selvin

Lecture 9 (February 14, 2011; Week 6)

Bioimage data analysis (III): Point feature detection, Part II; (IV) Edge detection

Canny PAMI paper

Why_use_Gaussian_kernel from Forsyth & Ponce, Computer vision: a modern approach, Prentice Hall, 2003.

Lecture 10 (February 21,2011; Week 7)

Bioimage data analysis (IV): Edge detection, line/curve detection

Canny edge detection MATLAB demo

Hough_transform_demo

PROJECT assignment 2 handout; (Ponti et al)
Lecture 11 (February 23, 2011; Week7)

Bioimage data analysis(IV): parametric transforms; Bioimage data analysis (V): thresholding-based segmentation (I)

Segmentation_demo_I

  
Lecture 12 (March 02, 2011; Week8)

Bioimage data analysis (V): thresholding-based segmentation (II); Introduction to ITK

  
Lecture 13 (March 14; Week 10)

Bioimage data analysis (V): region-based segmentation; watershed-based segmentation;graph-cut based segmentation

 

 
Lecture 14 (March 16, Week 10)

Bioimage data analysis (V) Graph-cut-based image segmentation; (VI) Particle tracking

Reading assignment 3 handout
Lecture 15 (March 21; Week 11) Bioimage data analysis (VI): Particle tracking (I)  
Lecture 16 (March 23, Week 11) Bioimage data analysis (VI): Particle tracking (II); (V): Active contour based image segmentation  
Lecture 17 (March 30, Week 12) Application case study (I): applications of particle detection and tracking techniques (I)  
Lecture 18 (April 4, Week 13) Application case study (I): applications of particle detection and tracking techniques (II)  
Lecture 19 (April 6, Week 13) Application case study (II): Electron microscopy; Super resolution fluorescence microscopy (I)  
Lecture 20 (Week 13) Application case study (II): Super resolution fluorescence microscopy (II)  
Lecture 21 (Week 14)  
Lecture 22 (Week 14) Molecular imaging  
Lecture 23 (Week 15) Project 3 presentation (II)  
Lecture 24 (Week 15)  
Lecture 25 (Week 16)    
Lecture 26 (Week 16) Bioimage database (bioimage information systems); Evaluation of bioimage analysis algorithms