Help Modulating Configurations for DNA Backbones

[neumagen]

Hello!

I normally use Gwyddion to flatten my .spm images using "level data by mean plane subtraction" and then "align rows" using the polynomial function before saving as a .tif and manually identifying the DNA backbones (output picture attached).

I am having some trouble figuring out all the configurations using TopoStats to best identify the backbones like I did in Gwyddion (picture attached with the suffix _above_masked).

I'm just looking for any insight as to which settings I should be adjusting in the configurations to achieve this!

Thanks