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. If you also want to align the images again, copy the images in raw_im in a new folder and run the code on that. For running only part of the code again, you need to delete the .trackOpti* files (note the period before, you’ll have to have the hidden files visible to see those) and run BatchSuperSeggerOpti with clean_flag = 0. The .trackOpti files are created during the different steps (they include the number of the step in their names). In order to run the find foci part of the code you need to delete ‘.trackOptiFindFociCyto-Step6.mat’ and all the steps after that which are : ‘.trackOptiClist-Step7.mat' and '.trackOptiCellFiles-Step8.mat'.