Hello, cardiac tissue engineers!

I am a cardiac tissue graduate student, I have fabricated a 50-um cardiac tissue with cardiomyocytes, and want to characterize it, I fixed and stained my tissue for a-actinin, and imaged through z-stacks by confocal microscopy, recorded around 30 frames with 2 um steps in the z-direction within the 60 um range. I want to perform image processing to quantify the sarcomere alignment. What's the best way of analyzing when sarcomeres alignment is not uniform through the thick tissue? Should I use max projection and go forward? any help would be appreciated! Thanks!

Paria