You recorded a data set with the Andor Ixon EMCCD. Now it is time to extract traces, with Matlab (data taken in D1.210). The required files are attached, save all of them to the same folder.
There are several steps in this process:
1. make a mapping file, which can be used to map the pixels in the red channel onto the same pixels in the green channel. Open autopick*.m, adapt the filename in the lines with 'filedir' and 'full', then run the matlab file.
In case you do not have a tetraspeack image for mapping, use a single molecule image, or even better an average on a sm image. As last resort, try manual alignment.
2. read in the images. Open matlab2c_v*, adapt the filename and run the Matlab file. It outputs a traces file which you can use for trace analysis.
Steps taken in Matlab2c_v* are:
* load in images from a stack
* transform the red channel
* Select interesting spots by thresholding
* Export each trace to a .traces file
Note: if your images look too noisy, you might want to explore the influence of spatial filtering.
Add im=gaussfilt(im) direclty after the line im=double(imread(filename,zz))