Handouts

Date Title Description
Lecture 1 (January 16, 2012) Introduction  
Lecture 2 (January 18, 2012)

Fundamentals of light microscopy

 
Lecture 3 (January 23, 2012)

 

Fundamentals of light microscopy (II); 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 25, 2012)

Practical issues in bioimage informatics (II); Fundamentals of fluorescence microscopy (I)

 
Lecture 5 (January 30, 2012) Fundamentals of fluorescence microscopy (continued); Bioimage data analysis (I): Basic operations

PROJECT assignment 1 handout

Image sequence download

Lecture 6 (February 1, 2012) Bioimage data analysis (I): Basic operations; Bioimage data analysis (II): Feature detection

Zitova&Flusser; Maintz&Viergever; Baker&Matthews

Lecture 7 (February 6, 2012) Bioimage data analysis (II): Point feature detection

READING assignment 2 handout

 

Lecture 8 (February 13, 2012)

Bioimage data analysis (II): Subpixel resolution point feature detection

Cheezum et al; Yildiz&Selvin

Lecture 9 (February 15, 2012)

Bioimage data analysis (II): Applications of point feature detection techniques

Canny PAMI paper

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

Lecture 10 (February 20, 2012)

Bioimage data analysis (II): Applications of point feature detection techniques, Super-resolution fluorescence imaging; Bioimage data analysis (III): Edge detection

 

Canny edge detection MATLAB demo

Hough_transform_demo

 
Lecture 11 (Febraray 22, 2012)

Bioimage data analysis(III): Edge detection; line/curve detection

Segmentation_demo_I

 
Lecture 12 (February 27, 2012)

Bioimage data analysis(III): line/curve detection; (IV): image segmentation (part 1)

 
Lecture 13 (February 29, 2012)

 

Bioimage data analysis (IV): image segmentation (part 2)

 

Lecture 14 (March 07, 2012)

Bioimage data anlaysis (IV): Image segmentation(part 3)

 
Lecture 15 (March 19, 2012)

Bioimage data analysis (IV): Image segmentation (part 4)

 
Lecture 16 (March 26, 2012)

Bioimage data analysis (IV): Image segmentation (part 5); Bioimage data analysis (V): Single particle tracking (part 1)

 
Lecture 17 (March 28, 2012) Bioimage data analysis (V): Single particle tracking (part 2)  
Lecture 18 (April 02, 2012) Bioimage data analysis (V): Single particle tracking (part 3)  
Lecture 19 (April 11, 2012) Biological application (I): Experimental and computational analysis of axonal transport  
Lecture 20 (April 16, 2012) Basic diffusion theory; Biological application (II): Experimental and computational analysis of spindle microtubule flux  
Lecture 21 (April 18, 2012) Biological application (III): High throughput / high content screens  
Lecture 22 (April 23, 2012) Empirical performance evaluaton of bioimage informatics algorithms; Image database, content-based image retrieval; Introduction to molecular imaging  
Lecture 23 (April 25, 2012) Molecular imaging  
Lecture 24 ()  
Lecture 25 ()    
Lecture 26 ()    
Lecture 27 ()    
Lecture 28 ()