(using FFT to) quantify sarcomere structures in 3D?

Sample image and/or macro code

Background

image showing saromere structures in 3D. I would like some advice on the best method on how to run and acquire quantification for outputs such as organisation and length.
Most literature points towards using FFT, but am open to using methods other than FFT also. Ideally something I can run with python, CellProfiler or ImageJ (or combination…)

Analysis goals

Sarcomere length
Sarcomere organisation

Challenges

Image size, complexity in 3D
Applying FFT to whole 3D image (not one ROI)
Understanding output files (what gives the length, organisation?)

  • What have you tried already?
    Colleague currently doing manual analysis on single ROI

  • What software packages and/or plugins have you tried?
    ImageJ