Explaining the folder structure

Each directory segmented by SuperSegger contains the following :

• raw_im : contains the raw images
• xy# : each xy frame has a separate folder
  • clist.mat : the clist matrix file
  • cell : contains all the cell files with information about each segmented cell
  • phase : contains the aligned phase images
  • fluor1 : contains the aligned fluorescence images for channel 1
  • fluor2 : contains the aligned fluorescence images for channel 2
  • seg
    • [name]_t*_seg.mat : created after first step of segmentation for time
    • [name]_t*_err.mat : created at the linking step of segmentation for time

The following files in the ‘seg’ directory are hidden and are used to continue the segmentation from the last successful step:

* .trackOptiStripSmall-Step1.mat: trackOptiStripSmall ran successfully
* .trackOptiLinkCell-Step2.mat: trackOptiLink ran successfully
* .trackOptiSkipMerge-Step2merge.mat: trackOptiSkipMerge ran successfully (only if skip>1)
* .trackOptiLinkCell-Step2merge.mat: trackOptiLink (if skip>1) ran successfully 
* .trackOptiFluor-Step4.mat: trackOptiFluor ran successfully
* .trackOptiMakeCell-Step5.mat: trackOptiMakeCell ran successfully
* .trackOptiCellMarker-Step3.mat: trackOptiCellMarker ran successfully 
* .trackOptiFindFoci-Step6.mat: trackOptiFindFoci ran successfully 
* .trackOptiClist-Step7.mat: trackOptiClist ran successfully
* .trackOptiCellFiles-Step8.mat: trackOptiCellFiles ran successfully

Tip for saving space :

The files needed at the end of segmentation for the viewer and analysis are the .err files, cell files and the clist. If you are satisfied with the segmentation and you would like to save space you can delete the .tif images in raw_im, phase, fluor folders and the seg/*seg.mat files. For the superSeggerViewer to be functional do not delete any of the folders, only their contents.