Matlab Tutorials

Matlab Introduction
Odes and Stochastics with Matlab
Image Analysis with Matlab

Images for analysis and Data

Phase and fluorescence images of E. coli cells


Fly elongation data


Cephallic furrow positioning images.


Image set for the matlab project.


Figure 2 from Rossi-Fanelli and Antonini (1958) for data extraction with DigitizeIt.

Figure 2A from Hoekstra et al. (2006) for data extraction with DigitizeIt.

 

Codes

Sunday - Random Walks, diffusion, and distributions
Introduction to Matlab and a 1D random walk.
Simulating diffusion across a synpatic cleft.
Simulating the binomial distribution.

Monday - Numerical integration and Matlab project part I
Numerical Integration of ligand-receptor binding.
Project part I: loading images, looking at histograms, and basic thresholding.

Tuesday - Statistical mechanics and Matlab project part II
Computing the probabilities of the promoter states of a regulated gene.
Project part II: Normailizing images, labeling regions, and extracting object properties.
Computing the probabilities of bound ligands in a cooperative system.
Simulating a genetic oscillator (not done in class).
Project part III: Filtering by area and generating overlay images.

Wednesday - MWC Model, elongation, the french flag model, and matlab project continued
Computing the statistical mechanical probabilites of the MWC model.
Measuring transcriptional elongation in Drosophila nuclei.
Measuring the relative positioning of the cephalic furrow in a Drosophila embryo.
Project part IV: Extracting fluorescence informaiton with a phase .

Thursday - Matlab project continued and fitting digitized data
The DigitizeIt project for Rossi-Finelli(1958) and the corresponding CSV file.
Curve fitting the digitized data and the BindingChiSq function.
Project part V: an automatic segmentation script and the two associated functions segmenter and extractor

Friday - Luria-Delbrück, the Kullback-Leibler divergence, Simpsons' paradox, and genetic drift.
Simulating the Luria-Delbrück fluctuation test.
The similarity between the Poisson and Binomial and calculation of the DKL.
Simpsons paradox in a microbial system (not coded in class).
Simulating genetic drift using a Moran process (not done in class).

Saturday - Finishing the Matlab project
A zip file of the script and two associated functions.