Re running the segmentation code

• If you wish to run the segmentation code again from the beginning other than the alignment set the clean flag to 1.

• To also align the images again, copy the images in raw_im in a new folder and run the code on that folder.

• For the code to continue from the last successful step if it is stopped abruptly, it creates some hidden files after every successful step. These files are in each xy directory, under the seg directory, and they have the format .trackOpti* (note the period before, you’ll have to have the hidden files visible to see those)

An easy way to run again specific steps of the code is to use the startEnd variable when you call BatchSuperSeggerOpti, with the clean_flag = 1. This will clean/remove all the selected steps in startEnd and run that code again. The startEnd accepts as the first entry the start step and as the second entry the end step (inclusive). The different steps and their numerical value are the following :

1 : alignment

2 : segmentation,

3 : stripping,

4 : linking,

5 : cell marker,

6 : fluor,

7 : foci,

8 : cellA structrues,

9 : clist,

10 : cell files.

For example, if you only want to run again the foci finding section, and you want those changed to be reflected in the cell files and clist, you can use :

% set dirname, and load constants of your choice
clean_flag = 1
skip = 1;
startEnd = [7 10];
BatchSuperSeggerOpti(dirname,skip,clean_flag,CONST,startEnd)