Adding an entry to the clist

To add a new entry to the clist, you have to modify the trackOptiClist.m code. Only variables (and their derivatives) calculated during segmentation and saved in the .seg/.err frame files can be added.

In this example we will add the fluorescence channel 3 (c4).

Navigate at the bottom of the file, where you will find the clistSetter with the different clist entries. The entries for fluor 2 look like these :

{'Fluor2 sum'},{'fl2sum'},0,1;

{'Fluor2 mean'},{'fl2sum./Area'},0,1;

The first entry is the name shown in the clist, the second the name of the variable, the third if it is calculated at birth, and the fourth if it is included in the time clist. Copy those entries at the end (just before the of the list '];') and change the fluor2 to fluor2 and fl2 to fl3:

{'Fluor3 sum'},{'fl3sum'},0,1;

{'Fluor3 mean'},{'fl3sum./Area'},0,1;

Next we should calculate fl3sum. Use control+F to find how fl2sum is extracted. You should find this line in the file

fl2sum = drill(data_c.CellA,'.fl2.sum');

Under this line, add a line for fluorescence 3 :

fl3sum = drill(data_c.CellA,'.fl3.sum');

When segmenting data from now on 'fl3sum' will be included in the clist produced by SuperSegger. In order to use the modified trackOptiClist on already segmented datasets, check the 'clean start end steps' and set 'start' : 9 and 'end' : 9 (9 is the clist step).