MATLAB 2011

Meets daily July 1 to July 15, 9:00-10:00, CRF Room 104 (July 5,12 in CRF 204)

Instructor: Prof. Keith Lidke

Room 1140, Physics and Astronomy
e-mail: klidke@unm.edu
phone: (505)277-0302

Getting Setup

DIPimage is a free image processing toolbox for MATLAB. We will use DIPimage throughout the course. You must download and install the appropriate version: DIPimage Download
Here is a beginning startup.m file: startup.m

Lecture Notes and Files

July 1: LecNote1.m ExScript1.m ExFunc1.m

July 5: LecNote2.m

July 6: LecNote3.m FitFunc.m SPTclass.m

July 7: LecNote4.m BlobMLE.m BlobMLE_Fast.m

July 8: LecNote5.m

July 11: LecNote6_SpotFind.m LecNote6_mex.m cMEXexample.c

July 12: PowerMeterExample.m LabJackReadAI.c LabJackSetDAC.c TestLabJack.m

July 13: cudaMEXexample.cu

Homework Assignments

HW#1: Find and plot the number of blobs versus frame number. Find and plot the mean value of the maximum intensity of the blobs versus frame number. Data: DataSet1.ics

HW#2: Generate an independently diffusing red and green blob in the same data set. Save the data to a MATLAB ".mat" file and make an ".avi" movie.

HW#3: Add to the SPTclass a method that performs the MSD calculation and a method that fits the MSD to extract D.

HW#4: Make a function that will find the center location of each blob in a 3D stack of blob images and return the found parameters x,y,N,bg for each image.

HW#5: Make a function that processes a 3D image stack to cut out fitting boxes from a series of images and returns them in a 3D stack that can be input into the function you created in HW#4. Add this function to the SPTclass.

HW#6: (1) Make a function that uses our found coordinates to cut out fitting boxes. Add this function to the SPTclass. (2) Implement BlobMLE_Fast.m as a mex fie.

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