## 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.

### More MATLAB Examples

DistributionExamples.m
CLTExample.m
FitExample.m
LSQfunc.m
CRLBExample.m
X2TestExample.m
GenRandomNumbers.m
GenPoisson.m
PoissonAsGauss.m
ErrorProp1.m
MultiVariateNormal.m
PredictiveInterval.m